@article{Tan2017,
  author={Tan, Tiong Yang and Dillon, Oliver James and Stark, Zornitza and Schofield, Deborah and Alam, Khurshid and Shrestha, Rupendra and Chong, Belinda and Phelan, Dean and Brett, Gemma R. and Creed, Emma and Jarmolowicz, Anna and Yap, Patrick and Walsh, Maie and Downie, Lilian and Amor, David J. and Savarirayan, Ravi and McGillivray, George and Yeung, Alison and Peters, Heidi and Robertson, Susan J. and Robinson, Aaron J. and Macciocca, Ivan and Sadedin, Simon and Bell, Katrina and Oshlack, Alicia and Georgeson, Peter and Thorne, Natalie and Gaff, Clara and White, Susan M.},
  title={Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions},
  journal={JAMA Pediatrics},
  year={2017},
  volume={171},
  pages={855},
  month={9},
  doi={10.1001/jamapediatrics.2017.1755}
}

@article{Clark2018,
  author={Clark, Michelle M. and Stark, Zornitza and Farnaes, Lauge and Tan, Tiong Y. and White, Susan M. and Dimmock, David and Kingsmore, Stephen F.},
  title={Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases},
  journal={npj Genomic Medicine},
  year={2018},
  volume={3},
  month={7},
  doi={10.1038/s41525-018-0053-8}
}

@article{Dai2022,
  author={Dai, Pei and Honda, Andrew and Ewans, Lisa and McGaughran, Julie and Burnett, Leslie and Law, Matthew and Phan, Tri Giang},
  title={Recommendations for next generation sequencing data reanalysis of unsolved cases with suspected Mendelian disorders: A systematic review and meta-analysis},
  journal={Genetics in Medicine},
  year={2022},
  volume={24},
  pages={1618--1629},
  month={8},
  doi={10.1016/j.gim.2022.04.021}
}

@article{TranMauThem2023,
  author={Tran Mau-Them, Fr\'{e}d\'{e}ric and Overs, Alexis and Bruel, Ange-Line and Duquet, Romain and Thareau, Mylene and Denomm\'{e}-Pichon, Anne-Sophie and Vitobello, Antonio and Sorlin, Arthur and Safraou, Hana and Nambot, Sophie and Delanne, Julian and Moutton, Sebastien and Racine, Caroline and Engel, Camille and De Giraud d'Agay, Melchior and Lehalle, Daphne and Goldenberg, Alice and Willems, Marjolaine and Coubes, Christine and Genevieve, David and Verloes, Alain and Capri, Yline and Perrin, Laurence and Jacquemont, Marie-Line and Lambert, Laetitia and Lacaze, Elodie and Thevenon, Julien and Hana, Nadine and Van-Gils, Julien and Dubucs, Charlotte and Bizaoui, Varoona and Gerard-Blanluet, Marion and Lespinasse, James and Mercier, Sandra and Guerrot, Anne-Marie and Maystadt, Isabelle and Tisserant, Emilie and Faivre, Laurence and Philippe, Christophe and Duffourd, Yannis and Thauvin-Robinet, Christel},
  title={Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis},
  journal={Frontiers in Genetics},
  year={2023},
  volume={14},
  month={4},
  doi={10.3389/fgene.2023.1122985}
}

@article{Yu2020,
  author={Yu, Zhenhua and Du, Fang and Ban, Rongjun and Zhang, Yuanwei},
  title={SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles},
  journal={BMC Bioinformatics},
  year={2020},
  volume={21},
  month={12},
  doi={10.1186/s12859-020-03665-5}
}

@article{Wang2015,
  author={Wang, Jing and Raskin, Leon and Samuels, David C. and Shyr, Yu and Guo, Yan},
  title={Genome measures used for quality control are dependent on gene function and ancestry},
  journal={Bioinformatics},
  year={2015},
  volume={31},
  pages={318--323},
  month={2},
  doi={10.1093/bioinformatics/btu668}
}

@article{Ewing2015,
  author={Ewing, Adam D and None, None and Houlahan, Kathleen E and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N and Bare, J Christopher and P'ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y and Kellen, Michael R and Norman, Thea C and Haussler, David and Friend, Stephen H and Stolovitzky, Gustavo and Margolin, Adam A and Stuart, Joshua M and Boutros, Paul C},
  title={Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection},
  journal={Nature Methods},
  year={2015},
  volume={12},
  pages={623--630},
  month={7},
  doi={10.1038/nmeth.3407}
}

@article{Olson2022,
  author={Olson, Nathan D. and Wagner, Justin and McDaniel, Jennifer and Stephens, Sarah H. and Westreich, Samuel T. and Prasanna, Anish G. and Johanson, Elaine and Boja, Emily and Maier, Ezekiel J. and Serang, Omar and J\'{a}spez, David and Lorenzo-Salazar, Jos\'{e} M. and Mu\ {n}oz-Barrera, Adri\'{a}n and Rubio-Rodr\'{\i}guez, Luis A. and Flores, Carlos and Kyriakidis, Konstantinos and Malousi, Andigoni and Shafin, Kishwar and Pesout, Trevor and Jain, Miten and Paten, Benedict and Chang, Pi-Chuan and Kolesnikov, Alexey and Nattestad, Maria and Baid, Gunjan and Goel, Sidharth and Yang, Howard and Carroll, Andrew and Eveleigh, Robert and Bourgey, Mathieu and Bourque, Guillaume and Li, Gen and Ma, ChouXian and Tang, LinQi and Du, YuanPing and Zhang, ShaoWei and Morata, Jordi and Tonda, Ra\'{u}l and Parra, Gen\'{\i}s and Trotta, Jean-R\'{e}mi and Brueffer, Christian and Demirkaya-Budak, Sinem and Kabakci-Zorlu, Duygu and Turgut, Deniz and Kalay, \"{O}zem and Budak, Gungor and Narc\i{}, K\"{u}bra and Arslan, Elif and Brown, Richard and Johnson, Ivan J. and Dolgoborodov, Alexey and Semenyuk, Vladimir and Jain, Amit and Tetikol, H. Serhat and Jain, Varun and Ruehle, Mike and Lajoie, Bryan and Roddey, Cooper and Catreux, Severine and Mehio, Rami and Ahsan, Mian Umair and Liu, Qian and Wang, Kai and Ebrahim Sahraeian, Sayed Mohammad and Fang, Li Tai and Mohiyuddin, Marghoob and Hung, Calvin and Jain, Chirag and Feng, Hanying and Li, Zhipan and Chen, Luoqi and Sedlazeck, Fritz J. and Zook, Justin M.},
  title={PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions},
  journal={Cell Genomics},
  year={2022},
  volume={2},
  pages={100129},
  month={5},
  doi={10.1016/j.xgen.2022.100129}
}

@article{VanDijk2014,
  author={van Dijk, Erwin L. and Jaszczyszyn, Yan and Thermes, Claude},
  title={Library preparation methods for next-generation sequencing: Tone down the bias},
  journal={Experimental Cell Research},
  year={2014},
  volume={322},
  pages={12--20},
  month={3},
  doi={10.1016/j.yexcr.2014.01.008}
}

@article{Head2014,
  author={Head, Steven R. and Komori, H. Kiyomi and LaMere, Sarah A. and Whisenant, Thomas and Van Nieuwerburgh, Filip and Salomon, Daniel R. and Ordoukhanian, Phillip},
  title={Library construction for next-generation sequencing: Overviews and challenges},
  journal={BioTechniques},
  year={2014},
  volume={56},
  pages={61--77},
  month={2},
  doi={10.2144/000114133}
}

@article{Anna2018,
  author={Anna, Abramowicz and Monika, Gos},
  title={Splicing mutations in human genetic disorders: examples, detection, and confirmation},
  journal={Journal of Applied Genetics},
  year={2018},
  volume={59},
  pages={253--268},
  month={8},
  doi={10.1007/s13353-018-0444-7}
}

@article{Plagnol2012,
  author={Plagnol, Vincent and Curtis, James and Epstein, Michael and Mok, Kin Y. and Stebbings, Emma and Grigoriadou, Sofia and Wood, Nicholas W. and Hambleton, Sophie and Burns, Siobhan O. and Thrasher, Adrian J. and Kumararatne, Dinakantha and Doffinger, Rainer and Nejentsev, Sergey},
  title={A robust model for read count data in exome sequencing experiments and implications for copy number variant calling},
  journal={Bioinformatics},
  year={2012},
  volume={28},
  pages={2747--2754},
  month={11},
  doi={10.1093/bioinformatics/bts526}
}

@article{Betschart2022,
  author={Betschart, Raphael O. and Thi\'{e}ry, Alexandre and Aguilera-Garcia, Domingo and Zoche, Martin and Moch, Holger and Twerenbold, Raphael and Zeller, Tanja and Blankenberg, Stefan and Ziegler, Andreas},
  title={Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment},
  journal={Scientific Reports},
  year={2022},
  volume={12},
  month={12},
  doi={10.1038/s41598-022-26181-3}
}

@article{Belkadi2015,
  author={Belkadi, Aziz and Bolze, Alexandre and Itan, Yuval and Cobat, Aur\'{e}lie and Vincent, Quentin B. and Antipenko, Alexander and Shang, Lei and Boisson, Bertrand and Casanova, Jean-Laurent and Abel, Laurent},
  title={Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants},
  journal={Proceedings of the National Academy of Sciences},
  year={2015},
  volume={112},
  pages={5473--5478},
  month={4},
  doi={10.1073/pnas.1418631112}
}

@article{Koboldt2012,
  author={Koboldt, Daniel C. and Zhang, Qunyuan and Larson, David E. and Shen, Dong and McLellan, Michael D. and Lin, Ling and Miller, Christopher A. and Mardis, Elaine R. and Ding, Li and Wilson, Richard K.},
  title={VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing},
  journal={Genome Research},
  year={2012},
  volume={22},
  pages={568--576},
  month={3},
  doi={10.1101/gr.129684.111}
}

@article{Wagner2022gene,
  author={Wagner, Justin and Olson, Nathan D. and Harris, Lindsay and McDaniel, Jennifer and Cheng, Haoyu and Fungtammasan, Arkarachai and Hwang, Yih-Chii and Gupta, Richa and Wenger, Aaron M. and Rowell, William J. and Khan, Ziad M. and Farek, Jesse and Zhu, Yiming and Pisupati, Aishwarya and Mahmoud, Medhat and Xiao, Chunlin and Yoo, Byunggil and Sahraeian, Sayed Mohammad Ebrahim and Miller, Danny E. and J\'{a}spez, David and Lorenzo-Salazar, Jos\'{e} M. and Mu\ {n}oz-Barrera, Adri\'{a}n and Rubio-Rodr\'{\i}guez, Luis A. and Flores, Carlos and Narzisi, Giuseppe and Evani, Uday Shanker and Clarke, Wayne E. and Lee, Joyce and Mason, Christopher E. and Lincoln, Stephen E. and Miga, Karen H. and Ebbert, Mark T. W. and Shumate, Alaina and Li, Heng and Chin, Chen-Shan and Zook, Justin M. and Sedlazeck, Fritz J.},
  title={Curated variation benchmarks for challenging medically relevant autosomal genes},
  journal={Nature Biotechnology},
  year={2022},
  volume={40},
  pages={672--680},
  month={5},
  doi={10.1038/s41587-021-01158-1}
}

@article{Li2021,
  author={Li, He and Dawood, Moez and Khayat, Michael M. and Farek, Jesse R. and Jhangiani, Shalini N. and Khan, Ziad M. and Mitani, Tadahiro and Coban-Akdemir, Zeynep and Lupski, James R. and Venner, Eric and Posey, Jennifer E. and Sabo, Aniko and Gibbs, Richard A.},
  title={Exome variant discrepancies due to reference-genome differences},
  journal={The American Journal of Human Genetics},
  year={2021},
  volume={108},
  pages={1239--1250},
  month={7},
  doi={10.1016/j.ajhg.2021.05.011}
}

@article{Alganmi2023,
  author={Alganmi, Nofe and Abusamra, Heba},
  title={Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools},
  journal={PLOS ONE},
  year={2023},
  volume={18},
  pages={e0288371},
  month={8},
  doi={10.1371/journal.pone.0288371}
}

@article{Carey,
  author={Carey, Louise and Nash, Benjamin M. and Wright, Dale C.},
  title={Molecular genetic studies of complete hydatidiform moles},
  journal={Translational Pediatrics},
  volume={4},
  doi={10.3978/j.issn.2224-4336.2015.04.02}
}

@inproceedings{Devresse2015,
  author={Devresse, Adrien and Delalondre, Fabien and Sch\"{u}rmann, Felix},
  title={Nix based fully automated workflows and ecosystem to guarantee scientific result reproducibility across software environments and systems},
  booktitle={SC15: The International Conference for High Performance Computing, Networking, Storage and Analysis},
  year={2015},
  month={11},
  publisher={ACM},
  doi={10.1145/2830168.2830172}
}

@article{Poplin2018,
  author={Poplin, Ryan and Chang, Pi-Chuan and Alexander, David and Schwartz, Scott and Colthurst, Thomas and Ku, Alexander and Newburger, Dan and Dijamco, Jojo and Nguyen, Nam and Afshar, Pegah T and Gross, Sam S and Dorfman, Lizzie and McLean, Cory Y and DePristo, Mark A},
  title={A universal SNP and small-indel variant caller using deep neural networks},
  journal={Nature Biotechnology},
  year={2018},
  volume={36},
  pages={983--987},
  month={11},
  doi={10.1038/nbt.4235}
}

@article{Beagan2021,
  author={Beagan, Jamie J. and Drees, Esther E.E. and Stathi, Phylicia and Eijk, Paul P. and Meulenbroeks, Laura and Kessler, Floortje and Middeldorp, Jaap M. and Pegtel, D. Michiel and Zijlstra, Jos\'{e}e M. and Sie, Daoud and Heideman, Dani\"{e}lle A.M. and Thunnissen, Erik and Smit, Linda and de Jong, Daphne and Mouliere, Florent and Ylstra, Bauke and Roemer, Margaretha G.M. and van Dijk, Erik},
  title={PCR-Free Shallow Whole Genome Sequencing for Chromosomal Copy Number Detection from Plasma of Cancer Patients Is an Efficient Alternative to the Conventional PCR-Based Approach},
  journal={The Journal of Molecular Diagnostics},
  year={2021},
  volume={23},
  pages={1553-1563},
  doi={10.1016/j.jmoldx.2021.08.008}
}

@article{Harrow,
  author={Harrow, Jennifer and Frankish, Adam and Gonzalez, Jose M. and Tapanari, Electra and Diekhans, Mark and Kokocinski, Felix and Aken, Bronwen L. and Barrell, Daniel and Zadissa, Amonida and Searle, Stephen and Barnes, If and Bignell, Alexandra and Boychenko, Veronika and Hunt, Toby and Kay, Mike and Mukherjee, Gaurab and Rajan, Jeena and Despacio-Reyes, Gloria and Saunders, Gary and Steward, Charles and Harte, Rachel and Lin, Michael and Howald, C\'{e}dric and Tanzer, Andrea and Derrien, Thomas and Chrast, Jacqueline and Walters, Nathalie and Balasubramanian, Suganthi and Pei, Baikang and Tress, Michael and Rodriguez, Jose Manuel and Ezkurdia, Iakes and van Baren, Jeltje and Brent, Michael and Haussler, David and Kellis, Manolis and Valencia, Alfonso and Reymond, Alexandre and Gerstein, Mark and Guig\'{o}, Roderic and Hubbard, Tim J.},
  title={GENCODE: The reference human genome annotation for The ENCODE Project},
  journal={Genome Research},
  volume={22},
  doi={10.1101/gr.135350.111}
}

@article{Hwang2019,
  author={Hwang, Kyu-Baek and Lee, In-Hee and Li, Honglan and Won, Dhong-Geon and Hernandez-Ferrer, Carles and Negron, Jose Alberto and Kong, Sek Won},
  title={Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings},
  journal={Scientific Reports},
  year={2019},
  volume={9},
  doi={10.1038/s41598-019-39108-2}
}

@article{Harpak2017,
  author={Harpak, Arbel and Lan, Xun and Gao, Ziyue and Pritchard, Jonathan K.},
  title={Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates},
  journal={Proceedings of the National Academy of Sciences},
  year={2017},
  volume={114},
  pages={12779--12784},
  month={11},
  doi={10.1073/pnas.1708151114}
}

@misc{Wagner2022,
  author={Wagner, Justin and Olson, Nathan D and Harris, Lindsay and McDaniel, Jennifer and Khan, Ziad and Farek, Jesse and Mahmoud, Medhat and Stankovic, Ana and Kovacevic, Vladimir and Yoo, Byunggil and Miller, Neil and Rosenfeld, Jeffrey A. and Ni, Bohan and Zarate, Samantha and Kirsche, Melanie and Aganezov, Sergey and Schatz, Michael and Narzisi, Giuseppe and Byrska-Bishop, Marta and Clarke, Wayne and Evani, Uday S. and Markello, Charles and Shafin, Kishwar and Zhou, Xin and Sidow, Arend and Bansal, Vikas and Ebert, Peter and Marschall, Tobias and Lansdorp, Peter and Hanlon, Vincent and Mattsson, Carl-Adam and Barrio, Alvaro Martinez and Fiddes, Ian T and Xiao, Chunlin and Fungtammasan, Arkarachai and Chin, Chen-Shan and Wenger, Aaron M and Rowell, William J and Sedlazeck, Fritz J and Carroll, Andrew and Salit, Marc and Zook, Justin M},
  title={Benchmarking challenging small variants with linked and long reads},
  month={7},
  year={2022},
  doi={10.1101/2020.07.24.212712},
  url={http://dx.doi.org/10.1101/2020.07.24.212712}
}

@article{Li2019,
  author={Li, Wentian and Freudenberg, Jerome and Freudenberg, Jan},
  title={Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome},
  journal={Gene},
  year={2019},
  volume={691},
  pages={141--152},
  month={4},
  doi={10.1016/j.gene.2018.12.040}
}

@article{DAurizio2016,
  author={D'Aurizio, Romina and Pippucci, Tommaso and Tattini, Lorenzo and Giusti, Betti and Pellegrini, Marco and Magi, Alberto},
  title={Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2},
  journal={Nucleic Acids Research},
  year={2016},
  pages={gkw695},
  month={8},
  doi={10.1093/nar/gkw695}
}

@misc{Poplin2017,
  author={Poplin, Ryan and Ruano-Rubio, Valentin and DePristo, Mark A. and Fennell, Tim J. and Carneiro, Mauricio O. and Van der Auwera, Geraldine A. and Kling, David E. and Gauthier, Laura D. and Levy-Moonshine, Ami and Roazen, David and Shakir, Khalid and Thibault, Joel and Chandran, Sheila and Whelan, Chris and Lek, Monkol and Gabriel, Stacey and Daly, Mark J and Neale, Ben and MacArthur, Daniel G. and Banks, Eric},
  title={Scaling accurate genetic variant discovery to tens of thousands of samples},
  month={11},
  year={2017},
  doi={10.1101/201178},
  url={http://dx.doi.org/10.1101/201178}
}

@article{Yang,
  author={Yang, Hui and Wang, Kai},
  title={Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR},
  journal={Nature Protocols},
  year={2015},
  volume={10},
  doi={10.1038/nprot.2015.105}
}

@article{Pan,
  author={Pan, Bohu and Kusko, Rebecca and Xiao, Wenming and Zheng, Yuanting and Liu, Zhichao and Xiao, Chunlin and Sakkiah, Sugunadevi and Guo, Wenjing and Gong, Ping and Zhang, Chaoyang and Ge, Weigong and Shi, Leming and Tong, Weida and Hong, Huixiao},
  title={Similarities and differences between variants called with human reference genome HG19 or HG38},
  journal={BMC Bioinformatics},
  volume={20},
  doi={10.1186/s12859-019-2620-0}
}

@article{Regier2018,
  author={Regier, Allison A. and Farjoun, Yossi and Larson, David E. and Krasheninina, Olga and Kang, Hyun Min and Howrigan, Daniel P. and Chen, Bo-Juen and Kher, Manisha and Banks, Eric and Ames, Darren C. and English, Adam C. and Li, Heng and Xing, Jinchuan and Zhang, Yeting and Matise, Tara and Abecasis, Goncalo R. and Salerno, Will and Zody, Michael C. and Neale, Benjamin M. and Hall, Ira M.},
  title={Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects},
  journal={Nature Communications},
  year={2018},
  volume={9},
  month={10},
  doi={10.1038/s41467-018-06159-4}
}

@article{Bedo2020,
  author={Bed\H{o}, Justin and Di Stefano, Leon and Papenfuss, Anthony T},
  title={Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix},
  journal={GigaScience},
  year={2020},
  volume={9},
  month={11},
  doi={10.1093/gigascience/giaa121}
}

@article{Thung2014,
  author={Thung, Djie Tjwan and de Ligt, Joep and Vissers, Lisenka EM and Steehouwer, Marloes and Kroon, Mark and de Vries, Petra and Slagboom, Eline P and Ye, Kai and Veltman, Joris A and Hehir-Kwa, Jayne Y},
  title={Mobster: accurate detection of mobile element insertions in next generation sequencing data},
  journal={Genome Biology},
  year={2014},
  volume={15},
  month={10},
  doi={10.1186/s13059-014-0488-x}
}

@article{AnnovarDoc,
  author={ANNOVAR},
  title={ANNOVAR documentation},
  year={2023},
  doi={10.1093/nar/gkz923/5603227}
}

@article{Zverinova2022,
  author={Zverinova, Stepanka and Guryev, Victor},
  title={Variant calling: Considerations, practices, and developments},
  journal={Human Mutation},
  year={2022},
  volume={43},
  pages={976--985},
  month={8},
  doi={10.1002/humu.24311}
}

@article{Baker2012,
  author={Baker, Monya},
  title={De novo genome assembly: what every biologist should know},
  journal={Nature Methods},
  year={2012},
  volume={9},
  pages={333--337},
  month={4},
  doi={10.1038/nmeth.1935}
}

@article{Olson,
  author={Olson, Nathan D. and Wagner, Justin and Dwarshuis, Nathan and Miga, Karen H. and Sedlazeck, Fritz J. and Salit, Marc and Zook, Justin M.},
  title={Variant calling and benchmarking in an era of complete human genome sequences},
  journal={Nature Reviews Genetics},
  doi={10.1038/s41576-023-00590-0}
}

@article{Dolzhenko2017,
  author={Dolzhenko, Egor and van Vugt, Joke J.F.A. and Shaw, Richard J. and Bekritsky, Mitchell A. and van Blitterswijk, Marka and Narzisi, Giuseppe and Ajay, Subramanian S. and Rajan, Vani and Lajoie, Bryan R. and Johnson, Nathan H. and Kingsbury, Zoya and Humphray, Sean J. and Schellevis, Raymond D. and Brands, William J. and Baker, Matt and Rademakers, Rosa and Kooyman, Maarten and Tazelaar, Gijs H.P. and van Es, Michael A. and McLaughlin, Russell and Sproviero, William and Shatunov, Aleksey and Jones, Ashley and Al Khleifat, Ahmad and Pittman, Alan and Morgan, Sarah and Hardiman, Orla and Al-Chalabi, Ammar and Shaw, Chris and Smith, Bradley and Neo, Edmund J. and Morrison, Karen and Shaw, Pamela J. and Reeves, Catherine and Winterkorn, Lara and Wexler, Nancy S. and Housman, David E. and Ng, Christopher W. and Li, Alina L. and Taft, Ryan J. and van den Berg, Leonard H. and Bentley, David R. and Veldink, Jan H. and Eberle, Michael A. and None, None},
  title={Detection of long repeat expansions from PCR-free whole-genome sequence data},
  journal={Genome Research},
  year={2017},
  volume={27},
  pages={1895--1903},
  month={11},
  doi={10.1101/gr.225672.117}
}

@article{Miga2014,
  author={Miga, Karen H. and Newton, Yulia and Jain, Miten and Altemose, Nicolas and Willard, Huntington F. and Kent, W. James},
  title={Centromere reference models for human chromosomes X and Y satellite arrays},
  journal={Genome Research},
  year={2014},
  volume={24},
  pages={697--707},
  month={4},
  doi={10.1101/gr.159624.113}
}

@article{Wetterstrand,
  author={Wetterstrand, Kris A.},
  title={DNA Sequencing Costs: Data}
}

@article{Kowalewski2022,
  author={Kowalewski, Markus and Seeber, Phillip},
  title={Sustainable packaging of quantum chemistry software with the Nix package manager},
  journal={International Journal of Quantum Chemistry},
  year={2022},
  volume={122},
  month={5},
  doi={10.1002/qua.26872}
}

@article{Koster2012,
  author={K\"{o}ster, Johannes and Rahmann, Sven},
  title={Snakemake\textemdash{}a scalable bioinformatics workflow engine},
  journal={Bioinformatics},
  year={2012},
  volume={28},
  pages={2520--2522},
  month={10},
  doi={10.1093/bioinformatics/bts480}
}

@article{Zook2019,
  author={Zook, Justin M. and McDaniel, Jennifer and Olson, Nathan D. and Wagner, Justin and Parikh, Hemang and Heaton, Haynes and Irvine, Sean A. and Trigg, Len and Truty, Rebecca and McLean, Cory Y. and De La Vega, Francisco M. and Xiao, Chunlin and Sherry, Stephen and Salit, Marc},
  title={An open resource for accurately benchmarking small variant and reference calls},
  journal={Nature Biotechnology},
  year={2019},
  volume={37},
  pages={561--566},
  month={5},
  doi={10.1038/s41587-019-0074-6}
}

@article{Musich2021,
  author={Musich, Ryan and Cadle-Davidson, Lance and Osier, Michael V.},
  title={Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider},
  journal={Frontiers in Plant Science},
  year={2021},
  volume={12},
  month={4},
  doi={10.3389/fpls.2021.657240}
}

@article{Souche2022,
  author={Souche, Erika and Beltran, Sergi and Brosens, Erwin and Belmont, John W. and Fossum, Magdalena and Riess, Olaf and Gilissen, Christian and Ardeshirdavani, Amin and Houge, Gunnar and van Gijn, Marielle and Clayton-Smith, Jill and Synofzik, Matthis and de Leeuw, Nicole and Deans, Zandra C. and Dincer, Yasemin and Eck, Sebastian H. and van der Crabben, Saskia and Balasubramanian, Meena and Graessner, Holm and Sturm, Marc and Firth, Helen and Ferlini, Alessandra and Nabbout, Rima and De Baere, Elfride and Liehr, Thomas and Macek, Milan and Matthijs, Gert and Scheffer, Hans and Bauer, Peter and Yntema, Helger G. and Weiss, Marjan M.},
  title={Recommendations for whole genome sequencing in diagnostics for rare diseases},
  journal={European Journal of Human Genetics},
  year={2022},
  volume={30},
  doi={10.1038/s41431-022-01113-x}
}

@article{Christophersen2017,
  author={Christophersen, Mikael K. and J\"{o}ud, Magnus and Ajore, Ram and Vege, Sunitha and Ljungdahl, Klara W. and Westhoff, Connie M. and Olsson, Martin L. and Storry, Jill R. and Nilsson, Bj\"{o}rn},
  title={SMIM1 variants rs1175550 and rs143702418 independently modulate Vel blood group antigen expression},
  journal={Scientific Reports},
  year={2017},
  volume={7},
  month={1},
  doi={10.1038/srep40451}
}

@misc{Cleary2015,
  author={Cleary, John G. and Braithwaite, Ross and Gaastra, Kurt and Hilbush, Brian S and Inglis, Stuart and Irvine, Sean A and Jackson, Alan and Littin, Richard and Rathod, Mehul and Ware, David and Zook, Justin M. and Trigg, Len and De La Vega, Francisco M.},
  title={Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines},
  month={8},
  year={2015},
  doi={10.1101/023754},
  url={http://dx.doi.org/10.1101/023754}
}

@article{Chen2019,
  author={Chen, Jiayun and Li, Xingsong and Zhong, Hongbin and Meng, Yuhuan and Du, Hongli},
  title={Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers},
  journal={Scientific Reports},
  year={2019},
  volume={9},
  doi={10.1038/s41598-019-45835-3}
}

@article{Kim2018,
  author={Kim, Sangtae and Scheffler, Konrad and Halpern, Aaron L. and Bekritsky, Mitchell A. and Noh, Eunho and K\"{a}llberg, Morten and Chen, Xiaoyu and Kim, Yeonbin and Beyter, Doruk and Krusche, Peter and Saunders, Christopher T.},
  title={Strelka2: fast and accurate calling of germline and somatic variants},
  journal={Nature Methods},
  year={2018},
  volume={15},
  pages={591--594},
  month={8},
  doi={10.1038/s41592-018-0051-x}
}

@article{Beck2016,
  author={Beck, Tyler F and Mullikin, James C and the NISC Comparative Sequencing Program, and Biesecker, Leslie G},
  title={Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants},
  journal={Clinical Chemistry},
  year={2016},
  volume={62},
  doi={10.1373/clinchem.2015.249623}
}

@article{Chen2016,
  author={Chen, Xiaoyu and Schulz-Trieglaff, Ole and Shaw, Richard and Barnes, Bret and Schlesinger, Felix and K\"{a}llberg, Morten and Cox, Anthony J. and Kruglyak, Semyon and Saunders, Christopher T.},
  title={Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications},
  journal={Bioinformatics},
  year={2016},
  volume={32},
  pages={1220--1222},
  month={4},
  doi={10.1093/bioinformatics/btv710}
}

@article{Rimmer2014,
  author={Rimmer, Andy and None, None and Phan, Hang and Mathieson, Iain and Iqbal, Zamin and Twigg, Stephen R F and Wilkie, Andrew O M and McVean, Gil and Lunter, Gerton},
  title={Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications},
  journal={Nature Genetics},
  year={2014},
  volume={46},
  pages={912--918},
  month={8},
  doi={10.1038/ng.3036}
}

@article{Donato2021,
  author={Donato, Luigi and Scimone, Concetta and Rinaldi, Carmela and D'Angelo, Rosalia and Sidoti, Antonina},
  title={New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies},
  journal={Neural Computing and Applications},
  year={2021},
  volume={33},
  pages={15669--15692},
  month={11},
  doi={10.1007/s00521-021-06188-z}
}

@article{Hwang2015,
  author={Hwang, Sohyun and Kim, Eiru and Lee, Insuk and Marcotte, Edward M.},
  title={Systematic comparison of variant calling pipelines using gold standard personal exome variants},
  journal={Scientific Reports},
  year={2015},
  volume={5},
  month={12},
  doi={10.1038/srep17875}
}

@article{Zook2016,
  author={Zook, Justin M. and Catoe, David and McDaniel, Jennifer and Vang, Lindsay and Spies, Noah and Sidow, Arend and Weng, Ziming and Liu, Yuling and Mason, Christopher E. and Alexander, Noah and Henaff, Elizabeth and McIntyre, Alexa B.R. and Chandramohan, Dhruva and Chen, Feng and Jaeger, Erich and Moshrefi, Ali and Pham, Khoa and Stedman, William and Liang, Tiffany and Saghbini, Michael and Dzakula, Zeljko and Hastie, Alex and Cao, Han and Deikus, Gintaras and Schadt, Eric and Sebra, Robert and Bashir, Ali and Truty, Rebecca M. and Chang, Christopher C. and Gulbahce, Natali and Zhao, Keyan and Ghosh, Srinka and Hyland, Fiona and Fu, Yutao and Chaisson, Mark and Xiao, Chunlin and Trow, Jonathan and Sherry, Stephen T. and Zaranek, Alexander W. and Ball, Madeleine and Bobe, Jason and Estep, Preston and Church, George M. and Marks, Patrick and Kyriazopoulou-Panagiotopoulou, Sofia and Zheng, Grace X.Y. and Schnall-Levin, Michael and Ordonez, Heather S. and Mudivarti, Patrice A. and Giorda, Kristina and Sheng, Ying and Rypdal, Karoline Bjarnesdatter and Salit, Marc},
  title={Extensive sequencing of seven human genomes to characterize benchmark reference materials},
  journal={Scientific Data},
  year={2016},
  volume={3},
  doi={10.1038/sdata.2016.25}
}

@article{Zook2020,
  author={Zook, Justin M. and Hansen, Nancy F. and Olson, Nathan D. and Chapman, Lesley and Mullikin, James C. and Xiao, Chunlin and Sherry, Stephen and Koren, Sergey and Phillippy, Adam M. and Boutros, Paul C. and Sahraeian, Sayed Mohammad E. and Huang, Vincent and Rouette, Alexandre and Alexander, Noah and Mason, Christopher E. and Hajirasouliha, Iman and Ricketts, Camir and Lee, Joyce and Tearle, Rick and Fiddes, Ian T. and Barrio, Alvaro Martinez and Wala, Jeremiah and Carroll, Andrew and Ghaffari, Noushin and Rodriguez, Oscar L. and Bashir, Ali and Jackman, Shaun and Farrell, John J. and Wenger, Aaron M. and Alkan, Can and Soylev, Arda and Schatz, Michael C. and Garg, Shilpa and Church, George and Marschall, Tobias and Chen, Ken and Fan, Xian and English, Adam C. and Rosenfeld, Jeffrey A. and Zhou, Weichen and Mills, Ryan E. and Sage, Jay M. and Davis, Jennifer R. and Kaiser, Michael D. and Oliver, John S. and Catalano, Anthony P. and Chaisson, Mark J. P. and Spies, Noah and Sedlazeck, Fritz J. and Salit, Marc},
  title={A robust benchmark for detection of germline large deletions and insertions},
  journal={Nature Biotechnology},
  year={2020},
  volume={38},
  pages={1347--1355},
  month={11},
  doi={10.1038/s41587-020-0538-8}
}

@article{Hu2021,
  author={Hu, Taishan and Chitnis, Nilesh and Monos, Dimitri and Dinh, Anh},
  title={Next-generation sequencing technologies: An overview},
  journal={Human Immunology},
  year={2021},
  volume={82},
  pages={801--811},
  month={11},
  doi={10.1016/j.humimm.2021.02.012}
}

@article{Matthijs2015,
  author={Matthijs, Gert and Souche, Erika and Alders, Mari\"{e}lle and Corveleyn, Anniek and Eck, Sebastian and Feenstra, Ilse and Race, Val\'{e}rie and Sistermans, Erik and Sturm, Marc and Weiss, Marjan and Yntema, Helger and Bakker, Egbert and Scheffer, Hans and Bauer, Peter},
  title={Guidelines for diagnostic next-generation sequencing},
  journal={European Journal of Human Genetics},
  year={2015},
  volume={24},
  doi={10.1038/ejhg.2015.226}
}

@article{Goodstadt,
  author={Goodstadt, Leo},
  title={Ruffus: a lightweight Python library for computational pipelines},
  journal={Bioinformatics},
  volume={26},
  doi={10.1093/bioinformatics/btq524}
}

@article{Li2018,
  author={Li, Heng and Bloom, Jonathan M. and Farjoun, Yossi and Fleharty, Mark and Gauthier, Laura and Neale, Benjamin and MacArthur, Daniel},
  title={A synthetic-diploid benchmark for accurate variant-calling evaluation},
  journal={Nature Methods},
  year={2018},
  volume={15},
  pages={595--597},
  month={8},
  doi={10.1038/s41592-018-0054-7}
}

@article{Ahmad2021,
  author={Ahmad, Tanveer and Al Ars, Zaid and Hofstee, H Peter},
  title={VC@Scale: Scalable and high-performance variant calling on cluster environments},
  journal={GigaScience},
  year={2021},
  volume={10},
  month={9},
  doi={10.1093/gigascience/giab057}
}

@article{DiTommaso2017,
  author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  title={Nextflow enables reproducible computational workflows},
  journal={Nature Biotechnology},
  year={2017},
  volume={35},
  pages={316--319},
  month={4},
  doi={10.1038/nbt.3820}
}

@article{Samuels2016,
  author={Samuels, David C and Wang, Jing and Ye, Fei and He, Jing and Levinson, Rebecca T and Sheng, Quanhu and Zhao, Shilin and Capra, John A and Shyr, Yu and Zheng, Wei and Guo, Yan},
  title={Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk},
  journal={Genetics},
  year={2016},
  volume={204},
  pages={893--904},
  month={11},
  doi={10.1534/genetics.116.189936}
}

@article{Duchene2015,
  author={Duch\^{e}ne, Sebasti\'{a}n and Ho, Simon YW and Holmes, Edward C},
  title={Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models},
  journal={BMC Evolutionary Biology},
  year={2015},
  volume={15},
  month={12},
  doi={10.1186/s12862-015-0312-6}
}

@article{Goodwin2016,
  author={Goodwin, Sara and McPherson, John D. and McCombie, W. Richard},
  title={Coming of age: ten years of next-generation sequencing technologies},
  journal={Nature Reviews Genetics},
  year={2016},
  volume={17},
  pages={333--351},
  month={6},
  doi={10.1038/nrg.2016.49}
}

@article{Leman2022,
  author={Leman, Rapha\"{e}l and Parfait, B\'{e}atrice and Vidaud, Dominique and Girodon, Emmanuelle and Pacot, Laurence and Le Gac, G\'{e}rald and Ka, Chandran and Ferec, Claude and Fichou, Yann and Quesnelle, C\'{e}line and Aucouturier, Camille and Muller, Etienne and Vaur, Dominique and Castera, Laurent and Boulouard, Flavie and Ricou, Agathe and Tubeuf, H\'{e}l\`{e}ne and Soukarieh, Omar and Gaildrat, Pascaline and Riant, Florence and Guillaud-Bataille, Marine and Caputo, Sandrine M. and Caux-Moncoutier, Virginie and Boutry-Kryza, Nadia and Bonnet-Dorion, Fran\c{c}oise and Schultz, Ines and Rossing, Maria and Quenez, Olivier and Goldenberg, Louis and Harter, Valentin and Parsons, Michael T. and Spurdle, Amanda B. and Fr\'{e}bourg, Thierry and Martins, Alexandra and Houdayer, Claude and Krieger, Sophie},
  title={SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing},
  journal={Human Mutation},
  year={2022},
  volume={43},
  pages={2308--2323},
  month={12},
  doi={10.1002/humu.24491}
}

@article{Duncavage2023,
  author={Duncavage, Eric J. and Coleman, Joshua F. and de Baca, Monica E. and Kadri, Sabah and Leon, Annette and Routbort, Mark and Roy, Somak and Suarez, Carlos J. and Vanderbilt, Chad and Zook, Justin M.},
  title={Recommendations for the Use of in Silico Approaches for Next-Generation Sequencing Bioinformatic Pipeline Validation},
  journal={The Journal of Molecular Diagnostics},
  year={2023},
  volume={25},
  pages={3--16},
  month={1},
  doi={10.1016/j.jmoldx.2022.09.007}
}

@article{Li2021Varben,
  author={Li, Ziyang and Fang, Shuangsang and Zhang, Rui and Yu, Lijia and Zhang, Jiawei and Bu, Dechao and Sun, Liang and Zhao, Yi and Li, Jinming},
  title={VarBen: Generating in Silico Reference Data Sets for Clinical Next-Generation Sequencing Bioinformatics Pipeline Evaluation},
  journal={The Journal of Molecular Diagnostics},
  year={2021},
  volume={23},
  pages={285-299},
  doi={10.1016/j.jmoldx.2020.11.010}
}

@article{Naud2008,
  author={Naud, Richard and Marcille, Nicolas and Clopath, Claudia and Gerstner, Wulfram},
  title={Firing patterns in the adaptive exponential integrate-and-fire model},
  journal={Biological Cybernetics},
  year={2008},
  volume={99},
  pages={335--347},
  month={11},
  doi={10.1007/s00422-008-0264-7}
}

@article{Verrou2022,
  author={Verrou, Kleio-Maria and Pavlopoulos, Georgios A. and Moulos, Panagiotis},
  title={Protocol for unbiased, consolidated variant calling from whole exome sequencing data},
  journal={STAR Protocols},
  year={2022},
  volume={3},
  pages={101418},
  month={6},
  doi={10.1016/j.xpro.2022.101418}
}

@article{Zhao2020,
  author={Zhao, Sen and Agafonov, Oleg and Azab, Abdulrahman and Stokowy, Tomasz and Hovig, Eivind},
  title={Accuracy and efficiency of germline variant calling pipelines for human genome data},
  journal={Scientific Reports},
  year={2020},
  volume={10},
  month={11},
  doi={10.1038/s41598-020-77218-4}
}

@article{1000Genomes,
  author={The 1000 Genomes Project Consortium},
  title={A global reference for human genetic variation},
  journal={Nature},
  year={2015},
  volume={526},
  pages={68--74},
  month={10},
  doi={10.1038/nature15393}
}

@article{Auwera2020,
  author={Van der Auwera, Geraldine A and O'Connor, Brian D.},
  title={Genomics in the cloud: using Docker, GATK, and WDL in Terra},
  year={2020}
}

@article{Eberle2017,
  author={Eberle, Michael A. and Fritzilas, Epameinondas and Krusche, Peter and K\"{a}llberg, Morten and Moore, Benjamin L. and Bekritsky, Mitchell A. and Iqbal, Zamin and Chuang, Han-Yu and Humphray, Sean J. and Halpern, Aaron L. and Kruglyak, Semyon and Margulies, Elliott H. and McVean, Gil and Bentley, David R.},
  title={A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree},
  journal={Genome Research},
  year={2017},
  volume={27},
  pages={157--164},
  month={1},
  doi={10.1101/gr.210500.116}
}

@article{Cingolani2012,
  author={Cingolani, Pablo and Platts, Adrian and Wang, Le Lily and Coon, Melissa and Nguyen, Tung and Wang, Luan and Land, Susan J. and Lu, Xiangyi and Ruden, Douglas M.},
  title={A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff},
  journal={Fly},
  year={2012},
  volume={6},
  pages={80--92},
  month={4},
  doi={10.4161/fly.19695}
}

@article{AustinTse2022,
  author={Austin-Tse, Christina A. and Jobanputra, Vaidehi and Perry, Denise L. and Bick, David and Taft, Ryan J. and Venner, Eric and Gibbs, Richard A. and Young, Ted and Barnett, Sarah and Belmont, John W. and Boczek, Nicole and Chowdhury, Shimul and Ellsworth, Katarzyna A. and Guha, Saurav and Kulkarni, Shashikant and Marcou, Cherisse and Meng, Linyan and Murdock, David R. and Rehman, Atteeq U. and Spiteri, Elizabeth and Thomas-Wilson, Amanda and Kearney, Hutton M. and Rehm, Heidi L. and None, None},
  title={Best practices for the interpretation and reporting of clinical whole genome sequencing},
  journal={npj Genomic Medicine},
  year={2022},
  volume={7},
  month={4},
  doi={10.1038/s41525-022-00295-z}
}

@article{Fida2023,
  author={Fida, Mariam and Sinan, Israa and Finan, Alan},
  title={Whole Exome Sequencing Achieved a Definite Diagnosis of Kaufman Oculocerebrofacial Syndrome in a Bahraini Family: A Case Report},
  journal={Clinical Medicine Insights: Pediatrics},
  year={2023},
  volume={17},
  month={1},
  doi={10.1177/11795565231200130}
}

@article{Firtina2016,
  author={Firtina, Can and Alkan, Can},
  title={On genomic repeats and reproducibility},
  journal={Bioinformatics},
  year={2016},
  volume={32},
  pages={2243--2247},
  month={8},
  doi={10.1093/bioinformatics/btw139}
}

@article{Amberger2015,
  author={Amberger, Joanna S. and Bocchini, Carol A. and Schiettecatte, Fran\c{c}ois and Scott, Alan F. and Hamosh, Ada},
  title={OMIM.org: Online Mendelian Inheritance in Man (OMIM\textregistered{}), an online catalog of human genes and genetic disorders},
  journal={Nucleic Acids Research},
  year={2015},
  volume={43},
  pages={D789--D798},
  month={1},
  doi={10.1093/nar/gku1205}
}

@article{Garcia2020,
  author={Garcia, Maxime and Juhos, Szilveszter and Larsson, Malin and Olason, Pall I. and Martin, Marcel and Eisfeldt, Jesper and DiLorenzo, Sebastian and Sandgren, Johanna and D\'{\i}az De St\aa{}hl, Teresita and Ewels, Philip and Wirta, Valtteri and Nist\'{e}r, Monica and K\"{a}ller, Max and Nystedt, Bj\"{o}rn},
  title={Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants},
  journal={F1000Research},
  year={2020},
  volume={9},
  pages={63},
  month={9},
  doi={10.12688/f1000research.16665.2}
}

@article{Jaganathan2019,
  author={Jaganathan, Kishore and Kyriazopoulou Panagiotopoulou, Sofia and McRae, Jeremy F. and Darbandi, Siavash Fazel and Knowles, David and Li, Yang I. and Kosmicki, Jack A. and Arbelaez, Juan and Cui, Wenwu and Schwartz, Grace B. and Chow, Eric D. and Kanterakis, Efstathios and Gao, Hong and Kia, Amirali and Batzoglou, Serafim and Sanders, Stephan J. and Farh, Kyle Kai-How},
  title={Predicting Splicing from Primary Sequence with Deep Learning},
  journal={Cell},
  year={2019},
  volume={176},
  pages={535--548.e24},
  month={1},
  doi={10.1016/j.cell.2018.12.015}
}

@article{Liao2023,
  author={Liao, Wen-Wei and Asri, Mobin and Ebler, Jana and Doerr, Daniel and Haukness, Marina and Hickey, Glenn and Lu, Shuangjia and Lucas, Julian K. and Monlong, Jean and Abel, Haley J. and Buonaiuto, Silvia and Chang, Xian H. and Cheng, Haoyu and Chu, Justin and Colonna, Vincenza and Eizenga, Jordan M. and Feng, Xiaowen and Fischer, Christian and Fulton, Robert S. and Garg, Shilpa and Groza, Cristian and Guarracino, Andrea and Harvey, William T. and Heumos, Simon and Howe, Kerstin and Jain, Miten and Lu, Tsung-Yu and Markello, Charles and Martin, Fergal J. and Mitchell, Matthew W. and Munson, Katherine M. and Mwaniki, Moses Njagi and Novak, Adam M. and Olsen, Hugh E. and Pesout, Trevor and Porubsky, David and Prins, Pjotr and Sibbesen, Jonas A. and Sir\'{e}n, Jouni and Tomlinson, Chad and Villani, Flavia and Vollger, Mitchell R. and Antonacci-Fulton, Lucinda L. and Baid, Gunjan and Baker, Carl A. and Belyaeva, Anastasiya and Billis, Konstantinos and Carroll, Andrew and Chang, Pi-Chuan and Cody, Sarah and Cook, Daniel E. and Cook-Deegan, Robert M. and Cornejo, Omar E. and Diekhans, Mark and Ebert, Peter and Fairley, Susan and Fedrigo, Olivier and Felsenfeld, Adam L. and Formenti, Giulio and Frankish, Adam and Gao, Yan and Garrison, Nanibaa' A. and Giron, Carlos Garcia and Green, Richard E. and Haggerty, Leanne and Hoekzema, Kendra and Hourlier, Thibaut and Ji, Hanlee P. and Kenny, Eimear E. and Koenig, Barbara A. and Kolesnikov, Alexey and Korbel, Jan O. and Kordosky, Jennifer and Koren, Sergey and Lee, HoJoon and Lewis, Alexandra P. and Magalh\ {a}es, Hugo and Marco-Sola, Santiago and Marijon, Pierre and McCartney, Ann and McDaniel, Jennifer and Mountcastle, Jacquelyn and Nattestad, Maria and Nurk, Sergey and Olson, Nathan D. and Popejoy, Alice B. and Puiu, Daniela and Rautiainen, Mikko and Regier, Allison A. and Rhie, Arang and Sacco, Samuel and Sanders, Ashley D. and Schneider, Valerie A. and Schultz, Baergen I. and Shafin, Kishwar and Smith, Michael W. and Sofia, Heidi J. and Abou Tayoun, Ahmad N. and Thibaud-Nissen, Fran\c{c}oise and Tricomi, Francesca Floriana and Wagner, Justin and Walenz, Brian and Wood, Jonathan M. D. and Zimin, Aleksey V. and Bourque, Guillaume and Chaisson, Mark J. P. and Flicek, Paul and Phillippy, Adam M. and Zook, Justin M. and Eichler, Evan E. and Haussler, David and Wang, Ting and Jarvis, Erich D. and Miga, Karen H. and Garrison, Erik and Marschall, Tobias and Hall, Ira M. and Li, Heng and Paten, Benedict},
  title={A draft human pangenome reference},
  journal={Nature},
  year={2023},
  volume={617},
  pages={312--324},
  month={5},
  doi={10.1038/s41586-023-05896-x}
}

@article{Roy2018,
  author={Roy, Somak and Coldren, Christopher and Karunamurthy, Arivarasan and Kip, Nefize S. and Klee, Eric W. and Lincoln, Stephen E. and Leon, Annette and Pullambhatla, Mrudula and Temple-Smolkin, Robyn L. and Voelkerding, Karl V. and Wang, Chen and Carter, Alexis B.},
  title={Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines},
  journal={The Journal of Molecular Diagnostics},
  year={2018},
  volume={20},
  pages={4--27},
  month={1},
  doi={10.1016/j.jmoldx.2017.11.003}
}

@article{Schneider2017,
  author={Schneider, Valerie A. and Graves-Lindsay, Tina and Howe, Kerstin and Bouk, Nathan and Chen, Hsiu-Chuan and Kitts, Paul A. and Murphy, Terence D. and Pruitt, Kim D. and Thibaud-Nissen, Fran\c{c}oise and Albracht, Derek and Fulton, Robert S. and Kremitzki, Milinn and Magrini, Vincent and Markovic, Chris and McGrath, Sean and Steinberg, Karyn Meltz and Auger, Kate and Chow, William and Collins, Joanna and Harden, Glenn and Hubbard, Timothy and Pelan, Sarah and Simpson, Jared T. and Threadgold, Glen and Torrance, James and Wood, Jonathan M. and Clarke, Laura and Koren, Sergey and Boitano, Matthew and Peluso, Paul and Li, Heng and Chin, Chen-Shan and Phillippy, Adam M. and Durbin, Richard and Wilson, Richard K. and Flicek, Paul and Eichler, Evan E. and Church, Deanna M.},
  title={Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly},
  journal={Genome Research},
  year={2017},
  volume={27},
  pages={849--864},
  month={5},
  doi={10.1101/gr.213611.116}
}

@article{Garrison2012,
  author={Garrison, Erik and Marth, Gabor},
  title={Haplotype-based variant detection from short-read sequencing},
  year={2012},
  month={Jul}
}

@article{Sorelle2020,
  author={SoRelle, Jeffrey A and Wachsmann, Megan and Cantarel, Brandi L.},
  title={Assembling and Validating Bioinformatic Pipelines for Next-Generation Sequencing Clinical Assays},
  journal={Archives of Pathology \textbackslash{}\& Laboratory Medicine},
  year={2020},
  volume={144},
  pages={1118--1130},
  month={9},
  doi={10.5858/arpa.2019-0476-ra}
}

@article{DeSainteAgathe,
  author={de Sainte Agathe, Jean-Madeleine and Filser, Mathilde and Isidor, Bertrand and Besnard, Thomas and Gueguen, Paul and Perrin, Aur\'{e}lien and Van Goethem, Charles and Verebi, Camille and Masingue, Marion and Rendu, John and Coss\'{e}e, Mireille and Bergougnoux, Anne and Frobert, Laurent and Buratti, Julien and Lejeune, \'{E}lodie and Le Guern, \'{E}ric and Pasquier, Florence and Clot, Fabienne and Kalatzis, Vasiliki and Roux, Anne-Fran\c{c}oise and Cogn\'{e}, Benjamin and Baux, David},
  title={SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation},
  journal={Human Genomics},
  volume={17},
  doi={10.1186/s40246-023-00451-1}
}

@article{Vivian2017,
  author={Vivian, John and Rao, Arjun Arkal and Nothaft, Frank Austin and Ketchum, Christopher and Armstrong, Joel and Novak, Adam and Pfeil, Jacob and Narkizian, Jake and Deran, Alden D and Musselman-Brown, Audrey and Schmidt, Hannes and Amstutz, Peter and Craft, Brian and Goldman, Mary and Rosenbloom, Kate and Cline, Melissa and O'Connor, Brian and Hanna, Megan and Birger, Chet and Kent, W James and Patterson, David A and Joseph, Anthony D and Zhu, Jingchun and Zaranek, Sasha and Getz, Gad and Haussler, David and Paten, Benedict},
  title={Toil enables reproducible, open source, big biomedical data analyses},
  journal={Nature Biotechnology},
  year={2017},
  volume={35},
  pages={314--316},
  month={4},
  doi={10.1038/nbt.3772}
}

@inbook{Ye2018,
  author={Ye, Kai and Guo, Li and Yang, Xiaofei and Lamijer, Eric-Wubbo and Raine, Keiran and Ning, Zemin},
  title={Split-Read Indel and Structural Variant Calling Using PINDEL},
  pages={95--105},
  publisher={Springer New York},
  year={2018},
  month={7},
  doi={10.1007/978-1-4939-8666-8\_7}
}

@article{Koboldt2009,
  author={Koboldt, Daniel C. and Chen, Ken and Wylie, Todd and Larson, David E. and McLellan, Michael D. and Mardis, Elaine R. and Weinstock, George M. and Wilson, Richard K. and Ding, Li},
  title={VarScan: variant detection in massively parallel sequencing of individual and pooled samples},
  journal={Bioinformatics},
  year={2009},
  volume={25},
  pages={2283--2285},
  month={9},
  doi={10.1093/bioinformatics/btp373}
}

@article{Cibulskis2013,
  author={Cibulskis, Kristian and Lawrence, Michael S and Carter, Scott L and Sivachenko, Andrey and Jaffe, David and Sougnez, Carrie and Gabriel, Stacey and Meyerson, Matthew and Lander, Eric S and Getz, Gad},
  title={Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples},
  journal={Nature Biotechnology},
  year={2013},
  volume={31},
  pages={213--219},
  month={3},
  doi={10.1038/nbt.2514}
}

@article{Jarvis2022,
  author={Jarvis, Erich D. and Formenti, Giulio and Rhie, Arang and Guarracino, Andrea and Yang, Chentao and Wood, Jonathan and Tracey, Alan and Thibaud-Nissen, Francoise and Vollger, Mitchell R. and Porubsky, David and Cheng, Haoyu and Asri, Mobin and Logsdon, Glennis A. and Carnevali, Paolo and Chaisson, Mark J. P. and Chin, Chen-Shan and Cody, Sarah and Collins, Joanna and Ebert, Peter and Escalona, Merly and Fedrigo, Olivier and Fulton, Robert S. and Fulton, Lucinda L. and Garg, Shilpa and Gerton, Jennifer L. and Ghurye, Jay and Granat, Anastasiya and Green, Richard E. and Harvey, William and Hasenfeld, Patrick and Hastie, Alex and Haukness, Marina and Jaeger, Erich B. and Jain, Miten and Kirsche, Melanie and Kolmogorov, Mikhail and Korbel, Jan O. and Koren, Sergey and Korlach, Jonas and Lee, Joyce and Li, Daofeng and Lindsay, Tina and Lucas, Julian and Luo, Feng and Marschall, Tobias and Mitchell, Matthew W. and McDaniel, Jennifer and Nie, Fan and Olsen, Hugh E. and Olson, Nathan D. and Pesout, Trevor and Potapova, Tamara and Puiu, Daniela and Regier, Allison and Ruan, Jue and Salzberg, Steven L. and Sanders, Ashley D. and Schatz, Michael C. and Schmitt, Anthony and Schneider, Valerie A. and Selvaraj, Siddarth and Shafin, Kishwar and Shumate, Alaina and Stitziel, Nathan O. and Stober, Catherine and Torrance, James and Wagner, Justin and Wang, Jianxin and Wenger, Aaron and Xiao, Chuanle and Zimin, Aleksey V. and Zhang, Guojie and Wang, Ting and Li, Heng and Garrison, Erik and Haussler, David and Hall, Ira and Zook, Justin M. and Eichler, Evan E. and Phillippy, Adam M. and Paten, Benedict and Howe, Kerstin and Miga, Karen H. and None, None},
  title={Semi-automated assembly of high-quality diploid human reference genomes},
  journal={Nature},
  year={2022},
  volume={611},
  pages={519--531},
  month={11},
  doi={10.1038/s41586-022-05325-5}
}

@article{Rhie2023,
  author={Rhie, Arang and Nurk, Sergey and Cechova, Monika and Hoyt, Savannah J. and Taylor, Dylan J. and Altemose, Nicolas and Hook, Paul W. and Koren, Sergey and Rautiainen, Mikko and Alexandrov, Ivan A. and Allen, Jamie and Asri, Mobin and Bzikadze, Andrey V. and Chen, Nae-Chyun and Chin, Chen-Shan and Diekhans, Mark and Flicek, Paul and Formenti, Giulio and Fungtammasan, Arkarachai and Garcia Giron, Carlos and Garrison, Erik and Gershman, Ariel and Gerton, Jennifer L. and Grady, Patrick G. S. and Guarracino, Andrea and Haggerty, Leanne and Halabian, Reza and Hansen, Nancy F. and Harris, Robert and Hartley, Gabrielle A. and Harvey, William T. and Haukness, Marina and Heinz, Jakob and Hourlier, Thibaut and Hubley, Robert M. and Hunt, Sarah E. and Hwang, Stephen and Jain, Miten and Kesharwani, Rupesh K. and Lewis, Alexandra P. and Li, Heng and Logsdon, Glennis A. and Lucas, Julian K. and Makalowski, Wojciech and Markovic, Christopher and Martin, Fergal J. and Mc Cartney, Ann M. and McCoy, Rajiv C. and McDaniel, Jennifer and McNulty, Brandy M. and Medvedev, Paul and Mikheenko, Alla and Munson, Katherine M. and Murphy, Terence D. and Olsen, Hugh E. and Olson, Nathan D. and Paulin, Luis F. and Porubsky, David and Potapova, Tamara and Ryabov, Fedor and Salzberg, Steven L. and Sauria, Michael E. G. and Sedlazeck, Fritz J. and Shafin, Kishwar and Shepelev, Valery A. and Shumate, Alaina and Storer, Jessica M. and Surapaneni, Likhitha and Taravella Oill, Angela M. and Thibaud-Nissen, Fran\c{c}oise and Timp, Winston and Tomaszkiewicz, Marta and Vollger, Mitchell R. and Walenz, Brian P. and Watwood, Allison C. and Weissensteiner, Matthias H. and Wenger, Aaron M. and Wilson, Melissa A. and Zarate, Samantha and Zhu, Yiming and Zook, Justin M. and Eichler, Evan E. and O'Neill, Rachel J. and Schatz, Michael C. and Miga, Karen H. and Makova, Kateryna D. and Phillippy, Adam M.},
  title={The complete sequence of a human Y chromosome},
  journal={Nature},
  year={2023},
  volume={621},
  pages={344--354},
  month={9},
  doi={10.1038/s41586-023-06457-y}
}

@article{Mclaren,
  author={McLaren, William and Gil, Laurent and Hunt, Sarah E. and Riat, Harpreet Singh and Ritchie, Graham R. S. and Thormann, Anja and Flicek, Paul and Cunningham, Fiona},
  title={The Ensembl Variant Effect Predictor},
  journal={Genome Biology},
  volume={17},
  doi={10.1186/s13059-016-0974-4}
}

@article{Pruitt,
  author={Pruitt, Kim D. and Brown, Garth R. and Hiatt, Susan M. and Thibaud-Nissen, Fran\c{c}oise and Astashyn, Alexander and Ermolaeva, Olga and Farrell, Catherine M. and Hart, Jennifer and Landrum, Melissa J. and McGarvey, Kelly M. and Murphy, Michael R. and O'Leary, Nuala A. and Pujar, Shashikant and Rajput, Bhanu and Rangwala, Sanjida H. and Riddick, Lillian D. and Shkeda, Andrei and Sun, Hanzhen and Tamez, Pamela and Tully, Raymond E. and Wallin, Craig and Webb, David and Weber, Janet and Wu, Wendy and DiCuccio, Michael and Kitts, Paul and Maglott, Donna R. and Murphy, Terence D. and Ostell, James M.},
  title={RefSeq: an update on mammalian reference sequences},
  journal={Nucleic Acids Research},
  volume={42},
  doi={10.1093/nar/gkt1114}
}

@article{Hardwick2017,
  author={Hardwick, Simon A. and Deveson, Ira W. and Mercer, Tim R.},
  title={Reference standards for next-generation sequencing},
  journal={Nature Reviews Genetics},
  year={2017},
  volume={18},
  pages={473--484},
  month={8},
  doi={10.1038/nrg.2017.44}
}

@article{Danecek2021,
  author={Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
  title={Twelve years of SAMtools and BCFtools},
  journal={GigaScience},
  year={2021},
  volume={10},
  month={1},
  doi={10.1093/gigascience/giab008}
}

@article{Miller2021,
  author={Miller, Thiago L A and Orpinelli Rego, Fernanda and Buzzo, Jos\'{e} Leonel L and Galante, Pedro A F},
  title={sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies},
  journal={Bioinformatics},
  year={2021},
  volume={37},
  pages={419--421},
  month={4},
  doi={10.1093/bioinformatics/btaa689}
}

@misc{Olson2020,
  author={Olson, Nathan D. and Wagner, Justin and McDaniel, Jennifer and Stephens, Sarah H. and Westreich, Samuel T. and Prasanna, Anish G. and Johanson, Elaine and Boja, Emily and Maier, Ezekiel J. and Serang, Omar and J\'{a}spez, David and Lorenzo-Salazar, Jos\'{e} M. and Mu\ {n}oz-Barrera, Adri\'{a}n and Rubio-Rodr\'{\i}guez, Luis A. and Flores, Carlos and Kyriakidis, Konstantinos and Malousi, Andigoni and Shafin, Kishwar and Pesout, Trevor and Jain, Miten and Paten, Benedict and Chang, Pi-Chuan and Kolesnikov, Alexey and Nattestad, Maria and Baid, Gunjan and Goel, Sidharth and Yang, Howard and Carroll, Andrew and Eveleigh, Robert and Bourgey, Mathieu and Bourque, Guillaume and Li, Gen and ChouXian, MA and Tang, LinQi and YuanPing, DU and Zhang, ShaoWei and Morata, Jordi and Tonda, Ra\'{u}l and Parra, Gen\'{\i}s and Trotta, Jean-R\'{e}mi and Brueffer, Christian and Demirkaya-Budak, Sinem and Kabakci-Zorlu, Duygu and Turgut, Deniz and Kalay, \"{O}zem and Budak, Gungor and Narc\i{}, K\"{u}bra and Arslan, Elif and Brown, Richard and Johnson, Ivan J and Dolgoborodov, Alexey and Semenyuk, Vladimir and Jain, Amit and Tetikol, H. Serhat and Jain, Varun and Ruehle, Mike and Lajoie, Bryan and Roddey, Cooper and Catreux, Severine and Mehio, Rami and Ahsan, Mian Umair and Liu, Qian and Wang, Kai and Sahraeian, Sayed Mohammad Ebrahim and Fang, Li Tai and Mohiyuddin, Marghoob and Hung, Calvin and Jain, Chirag and Feng, Hanying and Li, Zhipan and Chen, Luoqi and Sedlazeck, Fritz J. and Zook, Justin M.},
  title={precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions},
  month={11},
  year={2020},
  doi={10.1101/2020.11.13.380741},
  url={http://dx.doi.org/10.1101/2020.11.13.380741}
}

@article{Zook2014,
  author={Zook, Justin M and Chapman, Brad and Wang, Jason and Mittelman, David and Hofmann, Oliver and Hide, Winston and Salit, Marc},
  title={Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls},
  journal={Nature Biotechnology},
  year={2014},
  volume={32},
  pages={246--251},
  month={3},
  doi={10.1038/nbt.2835}
}

@article{Aganezov2022,
  author={Aganezov, Sergey and Yan, Stephanie M. and Soto, Daniela C. and Kirsche, Melanie and Zarate, Samantha and Avdeyev, Pavel and Taylor, Dylan J. and Shafin, Kishwar and Shumate, Alaina and Xiao, Chunlin and Wagner, Justin and McDaniel, Jennifer and Olson, Nathan D. and Sauria, Michael E. G. and Vollger, Mitchell R. and Rhie, Arang and Meredith, Melissa and Martin, Skylar and Lee, Joyce and Koren, Sergey and Rosenfeld, Jeffrey A. and Paten, Benedict and Layer, Ryan and Chin, Chen-Shan and Sedlazeck, Fritz J. and Hansen, Nancy F. and Miller, Danny E. and Phillippy, Adam M. and Miga, Karen H. and McCoy, Rajiv C. and Dennis, Megan Y. and Zook, Justin M. and Schatz, Michael C.},
  title={A complete reference genome improves analysis of human genetic variation},
  journal={Science},
  year={2022},
  volume={376},
  month={4},
  doi={10.1126/science.abl3533}
}

@inbook{Dolstra2004,
  author={Eelco Dolstra and Merijn de Jonge and Eelco Visser},
  title={Nix: A Safe and Policy-Free System for Software Deployment},
  year={2004}
}

@misc{Baid2020,
  author={Baid, Gunjan and Nattestad, Maria and Kolesnikov, Alexey and Goel, Sidharth and Yang, Howard and Chang, Pi-Chuan and Carroll, Andrew},
  title={An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development},
  month={12},
  year={2020},
  doi={10.1101/2020.12.11.422022},
  url={http://dx.doi.org/10.1101/2020.12.11.422022}
}

@article{Krusche2019,
  author={Krusche, Peter and None, None and Trigg, Len and Boutros, Paul C. and Mason, Christopher E. and De La Vega, Francisco M. and Moore, Benjamin L. and Gonzalez-Porta, Mar and Eberle, Michael A. and Tezak, Zivana and Lababidi, Samir and Truty, Rebecca and Asimenos, George and Funke, Birgit and Fleharty, Mark and Chapman, Brad A. and Salit, Marc and Zook, Justin M.},
  title={Best practices for benchmarking germline small-variant calls in human genomes},
  journal={Nature Biotechnology},
  year={2019},
  volume={37},
  pages={555--560},
  month={5},
  doi={10.1038/s41587-019-0054-x}
}

@article{Wang2010,
  author={Wang, Kai and Li, Mingyao and Hakonarson, Hakon},
  title={ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data},
  journal={Nucleic Acids Research},
  year={2010},
  volume={38},
  doi={10.1093/nar/gkq603}
}

@article{Pei2021,
  author={Pei, Surui and Liu, Tao and Ren, Xue and Li, Weizhong and Chen, Chongjian and Xie, Zhi},
  title={Benchmarking variant callers in next-generation and third-generation sequencing analysis},
  journal={Briefings in Bioinformatics},
  year={2021},
  volume={22},
  month={5},
  doi={10.1093/bib/bbaa148}
}

@article{Sherry2001,
  author={Sherry, S. T.},
  title={dbSNP: the NCBI database of genetic variation},
  journal={Nucleic Acids Research},
  year={2001},
  volume={29},
  pages={308--311},
  month={1},
  doi={10.1093/nar/29.1.308}
}

@article{Cameron2021,
  author={Cameron, Daniel L. and Baber, Jonathan and Shale, Charles and Valle-Inclan, Jose Espejo and Besselink, Nicolle and van Hoeck, Arne and Janssen, Roel and Cuppen, Edwin and Priestley, Peter and Papenfuss, Anthony T.},
  title={GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing},
  journal={Genome Biology},
  year={2021},
  volume={22},
  month={12},
  doi={10.1186/s13059-021-02423-x}
}

@article{Wilcox2021,
  author={Wilcox, Emma and Harrison, Steven M. and Lockhart, Edward and Voelkerding, Karl and Lubin, Ira M. and Rehm, Heidi L. and Kalman, Lisa V. and Funke, Birgit},
  title={Creation of an Expert Curated Variant List for Clinical Genomic Test Development and Validation},
  journal={The Journal of Molecular Diagnostics},
  year={2021},
  volume={23},
  pages={1500--1505},
  month={11},
  doi={10.1016/j.jmoldx.2021.07.018}
}

@article{Rausch2012,
  author={Rausch, Tobias and Zichner, Thomas and Schlattl, Andreas and St\"{u}tz, Adrian M. and Benes, Vladimir and Korbel, Jan O.},
  title={DELLY: structural variant discovery by integrated paired-end and split-read analysis},
  journal={Bioinformatics},
  year={2012},
  volume={28},
  pages={i333--i339},
  month={9},
  doi={10.1093/bioinformatics/bts378}
}

@article{Peyrard2008,
  author={Peyrard, T. and Pham, B.-N. and Le Pennec, P.-Y. and Rouger, P.},
  title={Les ph\'{e}notypes \'{e}rythrocytaires rares : un enjeu de sant\'{e} publique},
  journal={Transfusion Clinique et Biologique},
  year={2008},
  volume={15},
  pages={109--119},
  month={6},
  doi={10.1016/j.tracli.2008.02.001}
}

@article{Zeng2022,
  author={Zeng, Tony and Li, Yang I},
  title={Predicting RNA splicing from DNA sequence using Pangolin},
  journal={Genome Biology},
  year={2022},
  volume={23},
  doi={10.1186/s13059-022-02664-4}
}

@article{VanDerAuwera2013,
  author={Van der Auwera, Geraldine A. and Carneiro, Mauricio O. and Hartl, Christopher and Poplin, Ryan and del Angel, Guillermo and Levy-Moonshine, Ami and Jordan, Tadeusz and Shakir, Khalid and Roazen, David and Thibault, Joel and Banks, Eric and Garimella, Kiran V. and Altshuler, David and Gabriel, Stacey and DePristo, Mark A.},
  title={From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline},
  journal={Current Protocols in Bioinformatics},
  year={2013},
  volume={43},
  month={10},
  doi={10.1002/0471250953.bi1110s43}
}

@article{Landrum2016,
  author={Landrum, Melissa J. and Lee, Jennifer M. and Benson, Mark and Brown, Garth and Chao, Chen and Chitipiralla, Shanmuga and Gu, Baoshan and Hart, Jennifer and Hoffman, Douglas and Hoover, Jeffrey and Jang, Wonhee and Katz, Kenneth and Ovetsky, Michael and Riley, George and Sethi, Amanjeev and Tully, Ray and Villamarin-Salomon, Ricardo and Rubinstein, Wendy and Maglott, Donna R.},
  title={ClinVar: public archive of interpretations of clinically relevant variants},
  journal={Nucleic Acids Research},
  year={2016},
  volume={44},
  pages={D862--D868},
  month={1},
  doi={10.1093/nar/gkv1222}
}

@article{CofracSHGTA16,
  author={COFRAC},
  title={Guide technique d\textbackslash{}'accr\'{e}ditation de la technologie de s\'{e}quen\c{c}age \`{a} haut d\'{e}bit},
  year={2019}
}

@article{Barbitoff2022,
  author={Barbitoff, Yury A. and Abasov, Ruslan and Tvorogova, Varvara E. and Glotov, Andrey S. and Predeus, Alexander V.},
  title={Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery},
  journal={BMC Genomics},
  year={2022},
  volume={23},
  month={12},
  doi={10.1186/s12864-022-08365-3}
}

@article{Kumaran2019,
  author={Kumaran, Manojkumar and Subramanian, Umadevi and Devarajan, Bharanidharan},
  title={Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data},
  journal={BMC Bioinformatics},
  year={2019},
  volume={20},
  month={12},
  doi={10.1186/s12859-019-2928-9}
}

@article{Hatem2013,
  author={Hatem, Ayat and Bozda\u{g}, Doruk and Toland, Amanda E and \c{C}ataly\"{u}rek, \"{U}mit V},
  title={Benchmarking short sequence mapping tools},
  journal={BMC Bioinformatics},
  year={2013},
  volume={14},
  month={12},
  doi={10.1186/1471-2105-14-184}
}

@article{Jakobsen2019,
  author={Jakobsen, M. A. and Dellgren, C. and Sheppard, C. and Yazer, M. and Sprog\o{}e, U.},
  title={The use of next-generation sequencing for the determination of rare blood group genotypes},
  journal={Transfusion Medicine},
  year={2019},
  volume={29},
  pages={162--168},
  month={6},
  doi={10.1111/tme.12496}
}

@article{Nurk2022,
  author={Nurk, Sergey and Koren, Sergey and Rhie, Arang and Rautiainen, Mikko and Bzikadze, Andrey V. and Mikheenko, Alla and Vollger, Mitchell R. and Altemose, Nicolas and Uralsky, Lev and Gershman, Ariel and Aganezov, Sergey and Hoyt, Savannah J. and Diekhans, Mark and Logsdon, Glennis A. and Alonge, Michael and Antonarakis, Stylianos E. and Borchers, Matthew and Bouffard, Gerard G. and Brooks, Shelise Y. and Caldas, Gina V. and Chen, Nae-Chyun and Cheng, Haoyu and Chin, Chen-Shan and Chow, William and de Lima, Leonardo G. and Dishuck, Philip C. and Durbin, Richard and Dvorkina, Tatiana and Fiddes, Ian T. and Formenti, Giulio and Fulton, Robert S. and Fungtammasan, Arkarachai and Garrison, Erik and Grady, Patrick G. S. and Graves-Lindsay, Tina A. and Hall, Ira M. and Hansen, Nancy F. and Hartley, Gabrielle A. and Haukness, Marina and Howe, Kerstin and Hunkapiller, Michael W. and Jain, Chirag and Jain, Miten and Jarvis, Erich D. and Kerpedjiev, Peter and Kirsche, Melanie and Kolmogorov, Mikhail and Korlach, Jonas and Kremitzki, Milinn and Li, Heng and Maduro, Valerie V. and Marschall, Tobias and McCartney, Ann M. and McDaniel, Jennifer and Miller, Danny E. and Mullikin, James C. and Myers, Eugene W. and Olson, Nathan D. and Paten, Benedict and Peluso, Paul and Pevzner, Pavel A. and Porubsky, David and Potapova, Tamara and Rogaev, Evgeny I. and Rosenfeld, Jeffrey A. and Salzberg, Steven L. and Schneider, Valerie A. and Sedlazeck, Fritz J. and Shafin, Kishwar and Shew, Colin J. and Shumate, Alaina and Sims, Ying and Smit, Arian F. A. and Soto, Daniela C. and Sovi\'{c}, Ivan and Storer, Jessica M. and Streets, Aaron and Sullivan, Beth A. and Thibaud-Nissen, Fran\c{c}oise and Torrance, James and Wagner, Justin and Walenz, Brian P. and Wenger, Aaron and Wood, Jonathan M. D. and Xiao, Chunlin and Yan, Stephanie M. and Young, Alice C. and Zarate, Samantha and Surti, Urvashi and McCoy, Rajiv C. and Dennis, Megan Y. and Alexandrov, Ivan A. and Gerton, Jennifer L. and O'Neill, Rachel J. and Timp, Winston and Zook, Justin M. and Schatz, Michael C. and Eichler, Evan E. and Miga, Karen H. and Phillippy, Adam M.},
  title={The complete sequence of a human genome},
  journal={Science},
  year={2022},
  volume={376},
  pages={44--53},
  month={4},
  doi={10.1126/science.abj6987}
}

@article{Yen2017,
  author={Yen, Jennifer L. and Garcia, Sarah and Montana, Aldrin and Harris, Jason and Chervitz, Stephen and Morra, Massimo and West, John and Chen, Richard and Church, Deanna M.},
  title={A variant by any name: quantifying annotation discordance across tools and clinical databases},
  journal={Genome Medicine},
  year={2017},
  volume={9},
  doi={10.1186/s13073-016-0396-7}
}

@article{Vallet2022,
  author={Vallet, Nicolas and Michonneau, David and Tournier, Simon},
  title={Toward practical transparent verifiable and long-term reproducible research using Guix},
  journal={Scientific Data},
  year={2022},
  volume={9},
  month={10},
  doi={10.1038/s41597-022-01720-9}
}

@article{Alser2021,
  author={Alser, Mohammed and Rotman, Jeremy and Deshpande, Dhrithi and Taraszka, Kodi and Shi, Huwenbo and Baykal, Pelin Icer and Yang, Harry Taegyun and Xue, Victor and Knyazev, Sergey and Singer, Benjamin D. and Balliu, Brunilda and Koslicki, David and Skums, Pavel and Zelikovsky, Alex and Alkan, Can and Mutlu, Onur and Mangul, Serghei},
  title={Technology dictates algorithms: recent developments in read alignment},
  journal={Genome Biology},
  year={2021},
  volume={22},
  month={12},
  doi={10.1186/s13059-021-02443-7}
}

@article{ngsdiag2019,
  author={NGS-Diag},
  title={Qualification des solution bioinformatiques: note technique},
  year={2019}
}

@article{Li2009,
  author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and None, None},
  title={The Sequence Alignment/Map format and SAMtools},
  journal={Bioinformatics},
  year={2009},
  volume={25},
  pages={2078--2079},
  month={8},
  doi={10.1093/bioinformatics/btp352}
}

@article{Clark2018,
  author={Clark, Michelle M. and Stark, Zornitza and Farnaes, Lauge and Tan, Tiong Y. and White, Susan M. and Dimmock, David and Kingsmore, Stephen F.},
  title={Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases},
  journal={npj Genomic Medicine},
  year={2018},
  volume={3},
  month={7},
  doi={10.1038/s41525-018-0053-8}
}

@article{Tan2017,
  author={Tan, Tiong Yang and Dillon, Oliver James and Stark, Zornitza and Schofield, Deborah and Alam, Khurshid and Shrestha, Rupendra and Chong, Belinda and Phelan, Dean and Brett, Gemma R. and Creed, Emma and Jarmolowicz, Anna and Yap, Patrick and Walsh, Maie and Downie, Lilian and Amor, David J. and Savarirayan, Ravi and McGillivray, George and Yeung, Alison and Peters, Heidi and Robertson, Susan J. and Robinson, Aaron J. and Macciocca, Ivan and Sadedin, Simon and Bell, Katrina and Oshlack, Alicia and Georgeson, Peter and Thorne, Natalie and Gaff, Clara and White, Susan M.},
  title={Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions},
  journal={JAMA Pediatrics},
  year={2017},
  volume={171},
  pages={855},
  month={9},
  doi={10.1001/jamapediatrics.2017.1755}
}

@article{Dai2022,
  author={Dai, Pei and Honda, Andrew and Ewans, Lisa and McGaughran, Julie and Burnett, Leslie and Law, Matthew and Phan, Tri Giang},
  title={Recommendations for next generation sequencing data reanalysis of unsolved cases with suspected Mendelian disorders: A systematic review and meta-analysis},
  journal={Genetics in Medicine},
  year={2022},
  volume={24},
  pages={1618--1629},
  month={8},
  doi={10.1016/j.gim.2022.04.021}
}

@article{TranMauThem2023,
  author={Tran Mau-Them, Fr\'{e}d\'{e}ric and Overs, Alexis and Bruel, Ange-Line and Duquet, Romain and Thareau, Mylene and Denomm\'{e}-Pichon, Anne-Sophie and Vitobello, Antonio and Sorlin, Arthur and Safraou, Hana and Nambot, Sophie and Delanne, Julian and Moutton, Sebastien and Racine, Caroline and Engel, Camille and De Giraud d'Agay, Melchior and Lehalle, Daphne and Goldenberg, Alice and Willems, Marjolaine and Coubes, Christine and Genevieve, David and Verloes, Alain and Capri, Yline and Perrin, Laurence and Jacquemont, Marie-Line and Lambert, Laetitia and Lacaze, Elodie and Thevenon, Julien and Hana, Nadine and Van-Gils, Julien and Dubucs, Charlotte and Bizaoui, Varoona and Gerard-Blanluet, Marion and Lespinasse, James and Mercier, Sandra and Guerrot, Anne-Marie and Maystadt, Isabelle and Tisserant, Emilie and Faivre, Laurence and Philippe, Christophe and Duffourd, Yannis and Thauvin-Robinet, Christel},
  title={Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis},
  journal={Frontiers in Genetics},
  year={2023},
  volume={14},
  month={4},
  doi={10.3389/fgene.2023.1122985}
}

@article{Yu2020,
  author={Yu, Zhenhua and Du, Fang and Ban, Rongjun and Zhang, Yuanwei},
  title={SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles},
  journal={BMC Bioinformatics},
  year={2020},
  volume={21},
  month={12},
  doi={10.1186/s12859-020-03665-5}
}

@article{Wang2015,
  author={Wang, Jing and Raskin, Leon and Samuels, David C. and Shyr, Yu and Guo, Yan},
  title={Genome measures used for quality control are dependent on gene function and ancestry},
  journal={Bioinformatics},
  year={2015},
  volume={31},
  pages={318--323},
  month={2},
  doi={10.1093/bioinformatics/btu668}
}

@article{Ewing2015,
  author={Ewing, Adam D and None, None and Houlahan, Kathleen E and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N and Bare, J Christopher and P'ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y and Kellen, Michael R and Norman, Thea C and Haussler, David and Friend, Stephen H and Stolovitzky, Gustavo and Margolin, Adam A and Stuart, Joshua M and Boutros, Paul C},
  title={Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection},
  journal={Nature Methods},
  year={2015},
  volume={12},
  pages={623--630},
  month={7},
  doi={10.1038/nmeth.3407}
}

@article{Olson2022,
  author={Olson, Nathan D. and Wagner, Justin and McDaniel, Jennifer and Stephens, Sarah H. and Westreich, Samuel T. and Prasanna, Anish G. and Johanson, Elaine and Boja, Emily and Maier, Ezekiel J. and Serang, Omar and J\'{a}spez, David and Lorenzo-Salazar, Jos\'{e} M. and Mu\ {n}oz-Barrera, Adri\'{a}n and Rubio-Rodr\'{\i}guez, Luis A. and Flores, Carlos and Kyriakidis, Konstantinos and Malousi, Andigoni and Shafin, Kishwar and Pesout, Trevor and Jain, Miten and Paten, Benedict and Chang, Pi-Chuan and Kolesnikov, Alexey and Nattestad, Maria and Baid, Gunjan and Goel, Sidharth and Yang, Howard and Carroll, Andrew and Eveleigh, Robert and Bourgey, Mathieu and Bourque, Guillaume and Li, Gen and Ma, ChouXian and Tang, LinQi and Du, YuanPing and Zhang, ShaoWei and Morata, Jordi and Tonda, Ra\'{u}l and Parra, Gen\'{\i}s and Trotta, Jean-R\'{e}mi and Brueffer, Christian and Demirkaya-Budak, Sinem and Kabakci-Zorlu, Duygu and Turgut, Deniz and Kalay, \"{O}zem and Budak, Gungor and Narc\i{}, K\"{u}bra and Arslan, Elif and Brown, Richard and Johnson, Ivan J. and Dolgoborodov, Alexey and Semenyuk, Vladimir and Jain, Amit and Tetikol, H. Serhat and Jain, Varun and Ruehle, Mike and Lajoie, Bryan and Roddey, Cooper and Catreux, Severine and Mehio, Rami and Ahsan, Mian Umair and Liu, Qian and Wang, Kai and Ebrahim Sahraeian, Sayed Mohammad and Fang, Li Tai and Mohiyuddin, Marghoob and Hung, Calvin and Jain, Chirag and Feng, Hanying and Li, Zhipan and Chen, Luoqi and Sedlazeck, Fritz J. and Zook, Justin M.},
  title={PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions},
  journal={Cell Genomics},
  year={2022},
  volume={2},
  pages={100129},
  month={5},
  doi={10.1016/j.xgen.2022.100129}
}

@article{VanDijk2014,
  author={van Dijk, Erwin L. and Jaszczyszyn, Yan and Thermes, Claude},
  title={Library preparation methods for next-generation sequencing: Tone down the bias},
  journal={Experimental Cell Research},
  year={2014},
  volume={322},
  pages={12--20},
  month={3},
  doi={10.1016/j.yexcr.2014.01.008}
}

@article{Head2014,
  author={Head, Steven R. and Komori, H. Kiyomi and LaMere, Sarah A. and Whisenant, Thomas and Van Nieuwerburgh, Filip and Salomon, Daniel R. and Ordoukhanian, Phillip},
  title={Library construction for next-generation sequencing: Overviews and challenges},
  journal={BioTechniques},
  year={2014},
  volume={56},
  pages={61--77},
  month={2},
  doi={10.2144/000114133}
}

@article{Anna2018,
  author={Anna, Abramowicz and Monika, Gos},
  title={Splicing mutations in human genetic disorders: examples, detection, and confirmation},
  journal={Journal of Applied Genetics},
  year={2018},
  volume={59},
  pages={253--268},
  month={8},
  doi={10.1007/s13353-018-0444-7}
}

@article{Plagnol2012,
  author={Plagnol, Vincent and Curtis, James and Epstein, Michael and Mok, Kin Y. and Stebbings, Emma and Grigoriadou, Sofia and Wood, Nicholas W. and Hambleton, Sophie and Burns, Siobhan O. and Thrasher, Adrian J. and Kumararatne, Dinakantha and Doffinger, Rainer and Nejentsev, Sergey},
  title={A robust model for read count data in exome sequencing experiments and implications for copy number variant calling},
  journal={Bioinformatics},
  year={2012},
  volume={28},
  pages={2747--2754},
  month={11},
  doi={10.1093/bioinformatics/bts526}
}

@article{Betschart2022,
  author={Betschart, Raphael O. and Thi\'{e}ry, Alexandre and Aguilera-Garcia, Domingo and Zoche, Martin and Moch, Holger and Twerenbold, Raphael and Zeller, Tanja and Blankenberg, Stefan and Ziegler, Andreas},
  title={Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment},
  journal={Scientific Reports},
  year={2022},
  volume={12},
  month={12},
  doi={10.1038/s41598-022-26181-3}
}

@article{Belkadi2015,
  author={Belkadi, Aziz and Bolze, Alexandre and Itan, Yuval and Cobat, Aur\'{e}lie and Vincent, Quentin B. and Antipenko, Alexander and Shang, Lei and Boisson, Bertrand and Casanova, Jean-Laurent and Abel, Laurent},
  title={Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants},
  journal={Proceedings of the National Academy of Sciences},
  year={2015},
  volume={112},
  pages={5473--5478},
  month={4},
  doi={10.1073/pnas.1418631112}
}

@article{Koboldt2012,
  author={Koboldt, Daniel C. and Zhang, Qunyuan and Larson, David E. and Shen, Dong and McLellan, Michael D. and Lin, Ling and Miller, Christopher A. and Mardis, Elaine R. and Ding, Li and Wilson, Richard K.},
  title={VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing},
  journal={Genome Research},
  year={2012},
  volume={22},
  pages={568--576},
  month={3},
  doi={10.1101/gr.129684.111}
}

@article{Wagner2022gene,
  author={Wagner, Justin and Olson, Nathan D. and Harris, Lindsay and McDaniel, Jennifer and Cheng, Haoyu and Fungtammasan, Arkarachai and Hwang, Yih-Chii and Gupta, Richa and Wenger, Aaron M. and Rowell, William J. and Khan, Ziad M. and Farek, Jesse and Zhu, Yiming and Pisupati, Aishwarya and Mahmoud, Medhat and Xiao, Chunlin and Yoo, Byunggil and Sahraeian, Sayed Mohammad Ebrahim and Miller, Danny E. and J\'{a}spez, David and Lorenzo-Salazar, Jos\'{e} M. and Mu\ {n}oz-Barrera, Adri\'{a}n and Rubio-Rodr\'{\i}guez, Luis A. and Flores, Carlos and Narzisi, Giuseppe and Evani, Uday Shanker and Clarke, Wayne E. and Lee, Joyce and Mason, Christopher E. and Lincoln, Stephen E. and Miga, Karen H. and Ebbert, Mark T. W. and Shumate, Alaina and Li, Heng and Chin, Chen-Shan and Zook, Justin M. and Sedlazeck, Fritz J.},
  title={Curated variation benchmarks for challenging medically relevant autosomal genes},
  journal={Nature Biotechnology},
  year={2022},
  volume={40},
  pages={672--680},
  month={5},
  doi={10.1038/s41587-021-01158-1}
}

@article{Li2021,
  author={Li, He and Dawood, Moez and Khayat, Michael M. and Farek, Jesse R. and Jhangiani, Shalini N. and Khan, Ziad M. and Mitani, Tadahiro and Coban-Akdemir, Zeynep and Lupski, James R. and Venner, Eric and Posey, Jennifer E. and Sabo, Aniko and Gibbs, Richard A.},
  title={Exome variant discrepancies due to reference-genome differences},
  journal={The American Journal of Human Genetics},
  year={2021},
  volume={108},
  pages={1239--1250},
  month={7},
  doi={10.1016/j.ajhg.2021.05.011}
}

@article{Alganmi2023,
  author={Alganmi, Nofe and Abusamra, Heba},
  title={Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools},
  journal={PLOS ONE},
  year={2023},
  volume={18},
  pages={e0288371},
  month={8},
  doi={10.1371/journal.pone.0288371}
}

@article{Carey,
  author={Carey, Louise and Nash, Benjamin M. and Wright, Dale C.},
  title={Molecular genetic studies of complete hydatidiform moles},
  journal={Translational Pediatrics},
  volume={4},
  doi={10.3978/j.issn.2224-4336.2015.04.02}
}

@inproceedings{Devresse2015,
  author={Devresse, Adrien and Delalondre, Fabien and Sch\"{u}rmann, Felix},
  title={Nix based fully automated workflows and ecosystem to guarantee scientific result reproducibility across software environments and systems},
  booktitle={SC15: The International Conference for High Performance Computing, Networking, Storage and Analysis},
  year={2015},
  month={11},
  publisher={ACM},
  doi={10.1145/2830168.2830172}
}

@article{Poplin2018,
  author={Poplin, Ryan and Chang, Pi-Chuan and Alexander, David and Schwartz, Scott and Colthurst, Thomas and Ku, Alexander and Newburger, Dan and Dijamco, Jojo and Nguyen, Nam and Afshar, Pegah T and Gross, Sam S and Dorfman, Lizzie and McLean, Cory Y and DePristo, Mark A},
  title={A universal SNP and small-indel variant caller using deep neural networks},
  journal={Nature Biotechnology},
  year={2018},
  volume={36},
  pages={983--987},
  month={11},
  doi={10.1038/nbt.4235}
}

@article{Beagan2021,
  author={Beagan, Jamie J. and Drees, Esther E.E. and Stathi, Phylicia and Eijk, Paul P. and Meulenbroeks, Laura and Kessler, Floortje and Middeldorp, Jaap M. and Pegtel, D. Michiel and Zijlstra, Jos\'{e}e M. and Sie, Daoud and Heideman, Dani\"{e}lle A.M. and Thunnissen, Erik and Smit, Linda and de Jong, Daphne and Mouliere, Florent and Ylstra, Bauke and Roemer, Margaretha G.M. and van Dijk, Erik},
  title={PCR-Free Shallow Whole Genome Sequencing for Chromosomal Copy Number Detection from Plasma of Cancer Patients Is an Efficient Alternative to the Conventional PCR-Based Approach},
  journal={The Journal of Molecular Diagnostics},
  year={2021},
  volume={23},
  pages={1553-1563},
  doi={10.1016/j.jmoldx.2021.08.008}
}

@article{Harrow,
  author={Harrow, Jennifer and Frankish, Adam and Gonzalez, Jose M. and Tapanari, Electra and Diekhans, Mark and Kokocinski, Felix and Aken, Bronwen L. and Barrell, Daniel and Zadissa, Amonida and Searle, Stephen and Barnes, If and Bignell, Alexandra and Boychenko, Veronika and Hunt, Toby and Kay, Mike and Mukherjee, Gaurab and Rajan, Jeena and Despacio-Reyes, Gloria and Saunders, Gary and Steward, Charles and Harte, Rachel and Lin, Michael and Howald, C\'{e}dric and Tanzer, Andrea and Derrien, Thomas and Chrast, Jacqueline and Walters, Nathalie and Balasubramanian, Suganthi and Pei, Baikang and Tress, Michael and Rodriguez, Jose Manuel and Ezkurdia, Iakes and van Baren, Jeltje and Brent, Michael and Haussler, David and Kellis, Manolis and Valencia, Alfonso and Reymond, Alexandre and Gerstein, Mark and Guig\'{o}, Roderic and Hubbard, Tim J.},
  title={GENCODE: The reference human genome annotation for The ENCODE Project},
  journal={Genome Research},
  volume={22},
  doi={10.1101/gr.135350.111}
}

@article{Hwang2019,
  author={Hwang, Kyu-Baek and Lee, In-Hee and Li, Honglan and Won, Dhong-Geon and Hernandez-Ferrer, Carles and Negron, Jose Alberto and Kong, Sek Won},
  title={Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings},
  journal={Scientific Reports},
  year={2019},
  volume={9},
  doi={10.1038/s41598-019-39108-2}
}

@article{Harpak2017,
  author={Harpak, Arbel and Lan, Xun and Gao, Ziyue and Pritchard, Jonathan K.},
  title={Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates},
  journal={Proceedings of the National Academy of Sciences},
  year={2017},
  volume={114},
  pages={12779--12784},
  month={11},
  doi={10.1073/pnas.1708151114}
}

@misc{Wagner2022,
  author={Wagner, Justin and Olson, Nathan D and Harris, Lindsay and McDaniel, Jennifer and Khan, Ziad and Farek, Jesse and Mahmoud, Medhat and Stankovic, Ana and Kovacevic, Vladimir and Yoo, Byunggil and Miller, Neil and Rosenfeld, Jeffrey A. and Ni, Bohan and Zarate, Samantha and Kirsche, Melanie and Aganezov, Sergey and Schatz, Michael and Narzisi, Giuseppe and Byrska-Bishop, Marta and Clarke, Wayne and Evani, Uday S. and Markello, Charles and Shafin, Kishwar and Zhou, Xin and Sidow, Arend and Bansal, Vikas and Ebert, Peter and Marschall, Tobias and Lansdorp, Peter and Hanlon, Vincent and Mattsson, Carl-Adam and Barrio, Alvaro Martinez and Fiddes, Ian T and Xiao, Chunlin and Fungtammasan, Arkarachai and Chin, Chen-Shan and Wenger, Aaron M and Rowell, William J and Sedlazeck, Fritz J and Carroll, Andrew and Salit, Marc and Zook, Justin M},
  title={Benchmarking challenging small variants with linked and long reads},
  month={7},
  year={2022},
  doi={10.1101/2020.07.24.212712},
  url={http://dx.doi.org/10.1101/2020.07.24.212712}
}

@article{Li2019,
  author={Li, Wentian and Freudenberg, Jerome and Freudenberg, Jan},
  title={Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome},
  journal={Gene},
  year={2019},
  volume={691},
  pages={141--152},
  month={4},
  doi={10.1016/j.gene.2018.12.040}
}

@article{DAurizio2016,
  author={D'Aurizio, Romina and Pippucci, Tommaso and Tattini, Lorenzo and Giusti, Betti and Pellegrini, Marco and Magi, Alberto},
  title={Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2},
  journal={Nucleic Acids Research},
  year={2016},
  pages={gkw695},
  month={8},
  doi={10.1093/nar/gkw695}
}

@misc{Poplin2017,
  author={Poplin, Ryan and Ruano-Rubio, Valentin and DePristo, Mark A. and Fennell, Tim J. and Carneiro, Mauricio O. and Van der Auwera, Geraldine A. and Kling, David E. and Gauthier, Laura D. and Levy-Moonshine, Ami and Roazen, David and Shakir, Khalid and Thibault, Joel and Chandran, Sheila and Whelan, Chris and Lek, Monkol and Gabriel, Stacey and Daly, Mark J and Neale, Ben and MacArthur, Daniel G. and Banks, Eric},
  title={Scaling accurate genetic variant discovery to tens of thousands of samples},
  month={11},
  year={2017},
  doi={10.1101/201178},
  url={http://dx.doi.org/10.1101/201178}
}

@article{Yang2015,
  author={Yang, Hui and Wang, Kai},
  title={Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR},
  journal={Nature Protocols},
  year={2015},
  volume={10},
  doi={10.1038/nprot.2015.105}
}

@article{Pan,
  author={Pan, Bohu and Kusko, Rebecca and Xiao, Wenming and Zheng, Yuanting and Liu, Zhichao and Xiao, Chunlin and Sakkiah, Sugunadevi and Guo, Wenjing and Gong, Ping and Zhang, Chaoyang and Ge, Weigong and Shi, Leming and Tong, Weida and Hong, Huixiao},
  title={Similarities and differences between variants called with human reference genome HG19 or HG38},
  journal={BMC Bioinformatics},
  volume={20},
  doi={10.1186/s12859-019-2620-0}
}

@article{Regier2018,
  author={Regier, Allison A. and Farjoun, Yossi and Larson, David E. and Krasheninina, Olga and Kang, Hyun Min and Howrigan, Daniel P. and Chen, Bo-Juen and Kher, Manisha and Banks, Eric and Ames, Darren C. and English, Adam C. and Li, Heng and Xing, Jinchuan and Zhang, Yeting and Matise, Tara and Abecasis, Goncalo R. and Salerno, Will and Zody, Michael C. and Neale, Benjamin M. and Hall, Ira M.},
  title={Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects},
  journal={Nature Communications},
  year={2018},
  volume={9},
  month={10},
  doi={10.1038/s41467-018-06159-4}
}

@article{Bedo2020,
  author={Bed\H{o}, Justin and Di Stefano, Leon and Papenfuss, Anthony T},
  title={Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix},
  journal={GigaScience},
  year={2020},
  volume={9},
  month={11},
  doi={10.1093/gigascience/giaa121}
}

@article{Thung2014,
  author={Thung, Djie Tjwan and de Ligt, Joep and Vissers, Lisenka EM and Steehouwer, Marloes and Kroon, Mark and de Vries, Petra and Slagboom, Eline P and Ye, Kai and Veltman, Joris A and Hehir-Kwa, Jayne Y},
  title={Mobster: accurate detection of mobile element insertions in next generation sequencing data},
  journal={Genome Biology},
  year={2014},
  volume={15},
  month={10},
  doi={10.1186/s13059-014-0488-x}
}

@article{AnnovarDoc,
  author={ANNOVAR},
  title={ANNOVAR documentation},
  year={2023},
  doi={10.1093/nar/gkz923/5603227}
}

@article{Zverinova2022,
  author={Zverinova, Stepanka and Guryev, Victor},
  title={Variant calling: Considerations, practices, and developments},
  journal={Human Mutation},
  year={2022},
  volume={43},
  pages={976--985},
  month={8},
  doi={10.1002/humu.24311}
}

@article{Baker2012,
  author={Baker, Monya},
  title={De novo genome assembly: what every biologist should know},
  journal={Nature Methods},
  year={2012},
  volume={9},
  pages={333--337},
  month={4},
  doi={10.1038/nmeth.1935}
}

@article{Olson,
  author={Olson, Nathan D. and Wagner, Justin and Dwarshuis, Nathan and Miga, Karen H. and Sedlazeck, Fritz J. and Salit, Marc and Zook, Justin M.},
  title={Variant calling and benchmarking in an era of complete human genome sequences},
  journal={Nature Reviews Genetics},
  doi={10.1038/s41576-023-00590-0}
}

@article{Dolzhenko2017,
  author={Dolzhenko, Egor and van Vugt, Joke J.F.A. and Shaw, Richard J. and Bekritsky, Mitchell A. and van Blitterswijk, Marka and Narzisi, Giuseppe and Ajay, Subramanian S. and Rajan, Vani and Lajoie, Bryan R. and Johnson, Nathan H. and Kingsbury, Zoya and Humphray, Sean J. and Schellevis, Raymond D. and Brands, William J. and Baker, Matt and Rademakers, Rosa and Kooyman, Maarten and Tazelaar, Gijs H.P. and van Es, Michael A. and McLaughlin, Russell and Sproviero, William and Shatunov, Aleksey and Jones, Ashley and Al Khleifat, Ahmad and Pittman, Alan and Morgan, Sarah and Hardiman, Orla and Al-Chalabi, Ammar and Shaw, Chris and Smith, Bradley and Neo, Edmund J. and Morrison, Karen and Shaw, Pamela J. and Reeves, Catherine and Winterkorn, Lara and Wexler, Nancy S. and Housman, David E. and Ng, Christopher W. and Li, Alina L. and Taft, Ryan J. and van den Berg, Leonard H. and Bentley, David R. and Veldink, Jan H. and Eberle, Michael A. and None, None},
  title={Detection of long repeat expansions from PCR-free whole-genome sequence data},
  journal={Genome Research},
  year={2017},
  volume={27},
  pages={1895--1903},
  month={11},
  doi={10.1101/gr.225672.117}
}

@article{Miga2014,
  author={Miga, Karen H. and Newton, Yulia and Jain, Miten and Altemose, Nicolas and Willard, Huntington F. and Kent, W. James},
  title={Centromere reference models for human chromosomes X and Y satellite arrays},
  journal={Genome Research},
  year={2014},
  volume={24},
  pages={697--707},
  month={4},
  doi={10.1101/gr.159624.113}
}

@article{Wetterstrand,
  author={Wetterstrand, Kris A.},
  title={DNA Sequencing Costs: Data}
}

@article{Kowalewski2022,
  author={Kowalewski, Markus and Seeber, Phillip},
  title={Sustainable packaging of quantum chemistry software with the Nix package manager},
  journal={International Journal of Quantum Chemistry},
  year={2022},
  volume={122},
  month={5},
  doi={10.1002/qua.26872}
}

@article{Koster2012,
  author={K\"{o}ster, Johannes and Rahmann, Sven},
  title={Snakemake\textemdash{}a scalable bioinformatics workflow engine},
  journal={Bioinformatics},
  year={2012},
  volume={28},
  pages={2520--2522},
  month={10},
  doi={10.1093/bioinformatics/bts480}
}

@article{Zook2019,
  author={Zook, Justin M. and McDaniel, Jennifer and Olson, Nathan D. and Wagner, Justin and Parikh, Hemang and Heaton, Haynes and Irvine, Sean A. and Trigg, Len and Truty, Rebecca and McLean, Cory Y. and De La Vega, Francisco M. and Xiao, Chunlin and Sherry, Stephen and Salit, Marc},
  title={An open resource for accurately benchmarking small variant and reference calls},
  journal={Nature Biotechnology},
  year={2019},
  volume={37},
  pages={561--566},
  month={5},
  doi={10.1038/s41587-019-0074-6}
}

@article{Musich2021,
  author={Musich, Ryan and Cadle-Davidson, Lance and Osier, Michael V.},
  title={Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider},
  journal={Frontiers in Plant Science},
  year={2021},
  volume={12},
  month={4},
  doi={10.3389/fpls.2021.657240}
}

@article{Souche2022,
  author={Souche, Erika and Beltran, Sergi and Brosens, Erwin and Belmont, John W. and Fossum, Magdalena and Riess, Olaf and Gilissen, Christian and Ardeshirdavani, Amin and Houge, Gunnar and van Gijn, Marielle and Clayton-Smith, Jill and Synofzik, Matthis and de Leeuw, Nicole and Deans, Zandra C. and Dincer, Yasemin and Eck, Sebastian H. and van der Crabben, Saskia and Balasubramanian, Meena and Graessner, Holm and Sturm, Marc and Firth, Helen and Ferlini, Alessandra and Nabbout, Rima and De Baere, Elfride and Liehr, Thomas and Macek, Milan and Matthijs, Gert and Scheffer, Hans and Bauer, Peter and Yntema, Helger G. and Weiss, Marjan M.},
  title={Recommendations for whole genome sequencing in diagnostics for rare diseases},
  journal={European Journal of Human Genetics},
  year={2022},
  volume={30},
  doi={10.1038/s41431-022-01113-x}
}

@article{Christophersen2017,
  author={Christophersen, Mikael K. and J\"{o}ud, Magnus and Ajore, Ram and Vege, Sunitha and Ljungdahl, Klara W. and Westhoff, Connie M. and Olsson, Martin L. and Storry, Jill R. and Nilsson, Bj\"{o}rn},
  title={SMIM1 variants rs1175550 and rs143702418 independently modulate Vel blood group antigen expression},
  journal={Scientific Reports},
  year={2017},
  volume={7},
  month={1},
  doi={10.1038/srep40451}
}

@misc{Cleary2015,
  author={Cleary, John G. and Braithwaite, Ross and Gaastra, Kurt and Hilbush, Brian S and Inglis, Stuart and Irvine, Sean A and Jackson, Alan and Littin, Richard and Rathod, Mehul and Ware, David and Zook, Justin M. and Trigg, Len and De La Vega, Francisco M.},
  title={Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines},
  month={8},
  year={2015},
  doi={10.1101/023754},
  url={http://dx.doi.org/10.1101/023754}
}

@article{Chen2019,
  author={Chen, Jiayun and Li, Xingsong and Zhong, Hongbin and Meng, Yuhuan and Du, Hongli},
  title={Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers},
  journal={Scientific Reports},
  year={2019},
  volume={9},
  doi={10.1038/s41598-019-45835-3}
}

@article{Kim2018,
  author={Kim, Sangtae and Scheffler, Konrad and Halpern, Aaron L. and Bekritsky, Mitchell A. and Noh, Eunho and K\"{a}llberg, Morten and Chen, Xiaoyu and Kim, Yeonbin and Beyter, Doruk and Krusche, Peter and Saunders, Christopher T.},
  title={Strelka2: fast and accurate calling of germline and somatic variants},
  journal={Nature Methods},
  year={2018},
  volume={15},
  pages={591--594},
  month={8},
  doi={10.1038/s41592-018-0051-x}
}

@article{Beck2016,
  author={Beck, Tyler F and Mullikin, James C and the NISC Comparative Sequencing Program, and Biesecker, Leslie G},
  title={Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants},
  journal={Clinical Chemistry},
  year={2016},
  volume={62},
  doi={10.1373/clinchem.2015.249623}
}

@article{Chen2016,
  author={Chen, Xiaoyu and Schulz-Trieglaff, Ole and Shaw, Richard and Barnes, Bret and Schlesinger, Felix and K\"{a}llberg, Morten and Cox, Anthony J. and Kruglyak, Semyon and Saunders, Christopher T.},
  title={Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications},
  journal={Bioinformatics},
  year={2016},
  volume={32},
  pages={1220--1222},
  month={4},
  doi={10.1093/bioinformatics/btv710}
}

@article{Rimmer2014,
  author={Rimmer, Andy and None, None and Phan, Hang and Mathieson, Iain and Iqbal, Zamin and Twigg, Stephen R F and Wilkie, Andrew O M and McVean, Gil and Lunter, Gerton},
  title={Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications},
  journal={Nature Genetics},
  year={2014},
  volume={46},
  pages={912--918},
  month={8},
  doi={10.1038/ng.3036}
}

@article{Donato2021,
  author={Donato, Luigi and Scimone, Concetta and Rinaldi, Carmela and D'Angelo, Rosalia and Sidoti, Antonina},
  title={New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies},
  journal={Neural Computing and Applications},
  year={2021},
  volume={33},
  pages={15669--15692},
  month={11},
  doi={10.1007/s00521-021-06188-z}
}

@article{Hwang2015,
  author={Hwang, Sohyun and Kim, Eiru and Lee, Insuk and Marcotte, Edward M.},
  title={Systematic comparison of variant calling pipelines using gold standard personal exome variants},
  journal={Scientific Reports},
  year={2015},
  volume={5},
  month={12},
  doi={10.1038/srep17875}
}

@article{Zook2016,
  author={Zook, Justin M. and Catoe, David and McDaniel, Jennifer and Vang, Lindsay and Spies, Noah and Sidow, Arend and Weng, Ziming and Liu, Yuling and Mason, Christopher E. and Alexander, Noah and Henaff, Elizabeth and McIntyre, Alexa B.R. and Chandramohan, Dhruva and Chen, Feng and Jaeger, Erich and Moshrefi, Ali and Pham, Khoa and Stedman, William and Liang, Tiffany and Saghbini, Michael and Dzakula, Zeljko and Hastie, Alex and Cao, Han and Deikus, Gintaras and Schadt, Eric and Sebra, Robert and Bashir, Ali and Truty, Rebecca M. and Chang, Christopher C. and Gulbahce, Natali and Zhao, Keyan and Ghosh, Srinka and Hyland, Fiona and Fu, Yutao and Chaisson, Mark and Xiao, Chunlin and Trow, Jonathan and Sherry, Stephen T. and Zaranek, Alexander W. and Ball, Madeleine and Bobe, Jason and Estep, Preston and Church, George M. and Marks, Patrick and Kyriazopoulou-Panagiotopoulou, Sofia and Zheng, Grace X.Y. and Schnall-Levin, Michael and Ordonez, Heather S. and Mudivarti, Patrice A. and Giorda, Kristina and Sheng, Ying and Rypdal, Karoline Bjarnesdatter and Salit, Marc},
  title={Extensive sequencing of seven human genomes to characterize benchmark reference materials},
  journal={Scientific Data},
  year={2016},
  volume={3},
  doi={10.1038/sdata.2016.25}
}

@article{Zook2020,
  author={Zook, Justin M. and Hansen, Nancy F. and Olson, Nathan D. and Chapman, Lesley and Mullikin, James C. and Xiao, Chunlin and Sherry, Stephen and Koren, Sergey and Phillippy, Adam M. and Boutros, Paul C. and Sahraeian, Sayed Mohammad E. and Huang, Vincent and Rouette, Alexandre and Alexander, Noah and Mason, Christopher E. and Hajirasouliha, Iman and Ricketts, Camir and Lee, Joyce and Tearle, Rick and Fiddes, Ian T. and Barrio, Alvaro Martinez and Wala, Jeremiah and Carroll, Andrew and Ghaffari, Noushin and Rodriguez, Oscar L. and Bashir, Ali and Jackman, Shaun and Farrell, John J. and Wenger, Aaron M. and Alkan, Can and Soylev, Arda and Schatz, Michael C. and Garg, Shilpa and Church, George and Marschall, Tobias and Chen, Ken and Fan, Xian and English, Adam C. and Rosenfeld, Jeffrey A. and Zhou, Weichen and Mills, Ryan E. and Sage, Jay M. and Davis, Jennifer R. and Kaiser, Michael D. and Oliver, John S. and Catalano, Anthony P. and Chaisson, Mark J. P. and Spies, Noah and Sedlazeck, Fritz J. and Salit, Marc},
  title={A robust benchmark for detection of germline large deletions and insertions},
  journal={Nature Biotechnology},
  year={2020},
  volume={38},
  pages={1347--1355},
  month={11},
  doi={10.1038/s41587-020-0538-8}
}

@article{Hu2021,
  author={Hu, Taishan and Chitnis, Nilesh and Monos, Dimitri and Dinh, Anh},
  title={Next-generation sequencing technologies: An overview},
  journal={Human Immunology},
  year={2021},
  volume={82},
  pages={801--811},
  month={11},
  doi={10.1016/j.humimm.2021.02.012}
}

@article{Matthijs2015,
  author={Matthijs, Gert and Souche, Erika and Alders, Mari\"{e}lle and Corveleyn, Anniek and Eck, Sebastian and Feenstra, Ilse and Race, Val\'{e}rie and Sistermans, Erik and Sturm, Marc and Weiss, Marjan and Yntema, Helger and Bakker, Egbert and Scheffer, Hans and Bauer, Peter},
  title={Guidelines for diagnostic next-generation sequencing},
  journal={European Journal of Human Genetics},
  year={2015},
  volume={24},
  doi={10.1038/ejhg.2015.226}
}

@article{Goodstadt,
  author={Goodstadt, Leo},
  title={Ruffus: a lightweight Python library for computational pipelines},
  journal={Bioinformatics},
  volume={26},
  doi={10.1093/bioinformatics/btq524}
}

@article{Li2018,
  author={Li, Heng and Bloom, Jonathan M. and Farjoun, Yossi and Fleharty, Mark and Gauthier, Laura and Neale, Benjamin and MacArthur, Daniel},
  title={A synthetic-diploid benchmark for accurate variant-calling evaluation},
  journal={Nature Methods},
  year={2018},
  volume={15},
  pages={595--597},
  month={8},
  doi={10.1038/s41592-018-0054-7}
}

@article{Ahmad2021,
  author={Ahmad, Tanveer and Al Ars, Zaid and Hofstee, H Peter},
  title={VC@Scale: Scalable and high-performance variant calling on cluster environments},
  journal={GigaScience},
  year={2021},
  volume={10},
  month={9},
  doi={10.1093/gigascience/giab057}
}

@article{DiTommaso2017,
  author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  title={Nextflow enables reproducible computational workflows},
  journal={Nature Biotechnology},
  year={2017},
  volume={35},
  pages={316--319},
  month={4},
  doi={10.1038/nbt.3820}
}

@article{Samuels2016,
  author={Samuels, David C and Wang, Jing and Ye, Fei and He, Jing and Levinson, Rebecca T and Sheng, Quanhu and Zhao, Shilin and Capra, John A and Shyr, Yu and Zheng, Wei and Guo, Yan},
  title={Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk},
  journal={Genetics},
  year={2016},
  volume={204},
  pages={893--904},
  month={11},
  doi={10.1534/genetics.116.189936}
}

@article{Duchene2015,
  author={Duch\^{e}ne, Sebasti\'{a}n and Ho, Simon YW and Holmes, Edward C},
  title={Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models},
  journal={BMC Evolutionary Biology},
  year={2015},
  volume={15},
  month={12},
  doi={10.1186/s12862-015-0312-6}
}

@article{Goodwin2016,
  author={Goodwin, Sara and McPherson, John D. and McCombie, W. Richard},
  title={Coming of age: ten years of next-generation sequencing technologies},
  journal={Nature Reviews Genetics},
  year={2016},
  volume={17},
  pages={333--351},
  month={6},
  doi={10.1038/nrg.2016.49}
}

@article{Leman2022,
  author={Leman, Rapha\"{e}l and Parfait, B\'{e}atrice and Vidaud, Dominique and Girodon, Emmanuelle and Pacot, Laurence and Le Gac, G\'{e}rald and Ka, Chandran and Ferec, Claude and Fichou, Yann and Quesnelle, C\'{e}line and Aucouturier, Camille and Muller, Etienne and Vaur, Dominique and Castera, Laurent and Boulouard, Flavie and Ricou, Agathe and Tubeuf, H\'{e}l\`{e}ne and Soukarieh, Omar and Gaildrat, Pascaline and Riant, Florence and Guillaud-Bataille, Marine and Caputo, Sandrine M. and Caux-Moncoutier, Virginie and Boutry-Kryza, Nadia and Bonnet-Dorion, Fran\c{c}oise and Schultz, Ines and Rossing, Maria and Quenez, Olivier and Goldenberg, Louis and Harter, Valentin and Parsons, Michael T. and Spurdle, Amanda B. and Fr\'{e}bourg, Thierry and Martins, Alexandra and Houdayer, Claude and Krieger, Sophie},
  title={SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing},
  journal={Human Mutation},
  year={2022},
  volume={43},
  pages={2308--2323},
  month={12},
  doi={10.1002/humu.24491}
}

@article{Duncavage2023,
  author={Duncavage, Eric J. and Coleman, Joshua F. and de Baca, Monica E. and Kadri, Sabah and Leon, Annette and Routbort, Mark and Roy, Somak and Suarez, Carlos J. and Vanderbilt, Chad and Zook, Justin M.},
  title={Recommendations for the Use of in Silico Approaches for Next-Generation Sequencing Bioinformatic Pipeline Validation},
  journal={The Journal of Molecular Diagnostics},
  year={2023},
  volume={25},
  pages={3--16},
  month={1},
  doi={10.1016/j.jmoldx.2022.09.007}
}

@article{Li2021Varben,
  author={Li, Ziyang and Fang, Shuangsang and Zhang, Rui and Yu, Lijia and Zhang, Jiawei and Bu, Dechao and Sun, Liang and Zhao, Yi and Li, Jinming},
  title={VarBen: Generating in Silico Reference Data Sets for Clinical Next-Generation Sequencing Bioinformatics Pipeline Evaluation},
  journal={The Journal of Molecular Diagnostics},
  year={2021},
  volume={23},
  pages={285-299},
  doi={10.1016/j.jmoldx.2020.11.010}
}

@article{Naud2008,
  author={Naud, Richard and Marcille, Nicolas and Clopath, Claudia and Gerstner, Wulfram},
  title={Firing patterns in the adaptive exponential integrate-and-fire model},
  journal={Biological Cybernetics},
  year={2008},
  volume={99},
  pages={335--347},
  month={11},
  doi={10.1007/s00422-008-0264-7}
}

@article{Verrou2022,
  author={Verrou, Kleio-Maria and Pavlopoulos, Georgios A. and Moulos, Panagiotis},
  title={Protocol for unbiased, consolidated variant calling from whole exome sequencing data},
  journal={STAR Protocols},
  year={2022},
  volume={3},
  pages={101418},
  month={6},
  doi={10.1016/j.xpro.2022.101418}
}

@article{Zhao2020,
  author={Zhao, Sen and Agafonov, Oleg and Azab, Abdulrahman and Stokowy, Tomasz and Hovig, Eivind},
  title={Accuracy and efficiency of germline variant calling pipelines for human genome data},
  journal={Scientific Reports},
  year={2020},
  volume={10},
  month={11},
  doi={10.1038/s41598-020-77218-4}
}

@article{1000Genomes,
  author={The 1000 Genomes Project Consortium},
  title={A global reference for human genetic variation},
  journal={Nature},
  year={2015},
  volume={526},
  pages={68--74},
  month={10},
  doi={10.1038/nature15393}
}

@article{Auwera2020,
  author={Van der Auwera, Geraldine A and O'Connor, Brian D.},
  title={Genomics in the cloud: using Docker, GATK, and WDL in Terra},
  year={2020}
}

@article{Eberle2017,
  author={Eberle, Michael A. and Fritzilas, Epameinondas and Krusche, Peter and K\"{a}llberg, Morten and Moore, Benjamin L. and Bekritsky, Mitchell A. and Iqbal, Zamin and Chuang, Han-Yu and Humphray, Sean J. and Halpern, Aaron L. and Kruglyak, Semyon and Margulies, Elliott H. and McVean, Gil and Bentley, David R.},
  title={A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree},
  journal={Genome Research},
  year={2017},
  volume={27},
  pages={157--164},
  month={1},
  doi={10.1101/gr.210500.116}
}

@article{Cingolani2012,
  author={Cingolani, Pablo and Platts, Adrian and Wang, Le Lily and Coon, Melissa and Nguyen, Tung and Wang, Luan and Land, Susan J. and Lu, Xiangyi and Ruden, Douglas M.},
  title={A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff},
  journal={Fly},
  year={2012},
  volume={6},
  pages={80--92},
  month={4},
  doi={10.4161/fly.19695}
}

@article{AustinTse2022,
  author={Austin-Tse, Christina A. and Jobanputra, Vaidehi and Perry, Denise L. and Bick, David and Taft, Ryan J. and Venner, Eric and Gibbs, Richard A. and Young, Ted and Barnett, Sarah and Belmont, John W. and Boczek, Nicole and Chowdhury, Shimul and Ellsworth, Katarzyna A. and Guha, Saurav and Kulkarni, Shashikant and Marcou, Cherisse and Meng, Linyan and Murdock, David R. and Rehman, Atteeq U. and Spiteri, Elizabeth and Thomas-Wilson, Amanda and Kearney, Hutton M. and Rehm, Heidi L. and None, None},
  title={Best practices for the interpretation and reporting of clinical whole genome sequencing},
  journal={npj Genomic Medicine},
  year={2022},
  volume={7},
  month={4},
  doi={10.1038/s41525-022-00295-z}
}

@article{Fida2023,
  author={Fida, Mariam and Sinan, Israa and Finan, Alan},
  title={Whole Exome Sequencing Achieved a Definite Diagnosis of Kaufman Oculocerebrofacial Syndrome in a Bahraini Family: A Case Report},
  journal={Clinical Medicine Insights: Pediatrics},
  year={2023},
  volume={17},
  month={1},
  doi={10.1177/11795565231200130}
}

@article{Firtina2016,
  author={Firtina, Can and Alkan, Can},
  title={On genomic repeats and reproducibility},
  journal={Bioinformatics},
  year={2016},
  volume={32},
  pages={2243--2247},
  month={8},
  doi={10.1093/bioinformatics/btw139}
}

@article{Amberger2015,
  author={Amberger, Joanna S. and Bocchini, Carol A. and Schiettecatte, Fran\c{c}ois and Scott, Alan F. and Hamosh, Ada},
  title={OMIM.org: Online Mendelian Inheritance in Man (OMIM\textregistered{}), an online catalog of human genes and genetic disorders},
  journal={Nucleic Acids Research},
  year={2015},
  volume={43},
  pages={D789--D798},
  month={1},
  doi={10.1093/nar/gku1205}
}

@article{Garcia2020,
  author={Garcia, Maxime and Juhos, Szilveszter and Larsson, Malin and Olason, Pall I. and Martin, Marcel and Eisfeldt, Jesper and DiLorenzo, Sebastian and Sandgren, Johanna and D\'{\i}az De St\aa{}hl, Teresita and Ewels, Philip and Wirta, Valtteri and Nist\'{e}r, Monica and K\"{a}ller, Max and Nystedt, Bj\"{o}rn},
  title={Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants},
  journal={F1000Research},
  year={2020},
  volume={9},
  pages={63},
  month={9},
  doi={10.12688/f1000research.16665.2}
}

@article{Jaganathan2019,
  author={Jaganathan, Kishore and Kyriazopoulou Panagiotopoulou, Sofia and McRae, Jeremy F. and Darbandi, Siavash Fazel and Knowles, David and Li, Yang I. and Kosmicki, Jack A. and Arbelaez, Juan and Cui, Wenwu and Schwartz, Grace B. and Chow, Eric D. and Kanterakis, Efstathios and Gao, Hong and Kia, Amirali and Batzoglou, Serafim and Sanders, Stephan J. and Farh, Kyle Kai-How},
  title={Predicting Splicing from Primary Sequence with Deep Learning},
  journal={Cell},
  year={2019},
  volume={176},
  pages={535--548.e24},
  month={1},
  doi={10.1016/j.cell.2018.12.015}
}

@article{Liao2023,
  author={Liao, Wen-Wei and Asri, Mobin and Ebler, Jana and Doerr, Daniel and Haukness, Marina and Hickey, Glenn and Lu, Shuangjia and Lucas, Julian K. and Monlong, Jean and Abel, Haley J. and Buonaiuto, Silvia and Chang, Xian H. and Cheng, Haoyu and Chu, Justin and Colonna, Vincenza and Eizenga, Jordan M. and Feng, Xiaowen and Fischer, Christian and Fulton, Robert S. and Garg, Shilpa and Groza, Cristian and Guarracino, Andrea and Harvey, William T. and Heumos, Simon and Howe, Kerstin and Jain, Miten and Lu, Tsung-Yu and Markello, Charles and Martin, Fergal J. and Mitchell, Matthew W. and Munson, Katherine M. and Mwaniki, Moses Njagi and Novak, Adam M. and Olsen, Hugh E. and Pesout, Trevor and Porubsky, David and Prins, Pjotr and Sibbesen, Jonas A. and Sir\'{e}n, Jouni and Tomlinson, Chad and Villani, Flavia and Vollger, Mitchell R. and Antonacci-Fulton, Lucinda L. and Baid, Gunjan and Baker, Carl A. and Belyaeva, Anastasiya and Billis, Konstantinos and Carroll, Andrew and Chang, Pi-Chuan and Cody, Sarah and Cook, Daniel E. and Cook-Deegan, Robert M. and Cornejo, Omar E. and Diekhans, Mark and Ebert, Peter and Fairley, Susan and Fedrigo, Olivier and Felsenfeld, Adam L. and Formenti, Giulio and Frankish, Adam and Gao, Yan and Garrison, Nanibaa' A. and Giron, Carlos Garcia and Green, Richard E. and Haggerty, Leanne and Hoekzema, Kendra and Hourlier, Thibaut and Ji, Hanlee P. and Kenny, Eimear E. and Koenig, Barbara A. and Kolesnikov, Alexey and Korbel, Jan O. and Kordosky, Jennifer and Koren, Sergey and Lee, HoJoon and Lewis, Alexandra P. and Magalh\ {a}es, Hugo and Marco-Sola, Santiago and Marijon, Pierre and McCartney, Ann and McDaniel, Jennifer and Mountcastle, Jacquelyn and Nattestad, Maria and Nurk, Sergey and Olson, Nathan D. and Popejoy, Alice B. and Puiu, Daniela and Rautiainen, Mikko and Regier, Allison A. and Rhie, Arang and Sacco, Samuel and Sanders, Ashley D. and Schneider, Valerie A. and Schultz, Baergen I. and Shafin, Kishwar and Smith, Michael W. and Sofia, Heidi J. and Abou Tayoun, Ahmad N. and Thibaud-Nissen, Fran\c{c}oise and Tricomi, Francesca Floriana and Wagner, Justin and Walenz, Brian and Wood, Jonathan M. D. and Zimin, Aleksey V. and Bourque, Guillaume and Chaisson, Mark J. P. and Flicek, Paul and Phillippy, Adam M. and Zook, Justin M. and Eichler, Evan E. and Haussler, David and Wang, Ting and Jarvis, Erich D. and Miga, Karen H. and Garrison, Erik and Marschall, Tobias and Hall, Ira M. and Li, Heng and Paten, Benedict},
  title={A draft human pangenome reference},
  journal={Nature},
  year={2023},
  volume={617},
  pages={312--324},
  month={5},
  doi={10.1038/s41586-023-05896-x}
}

@article{Roy2018,
  author={Roy, Somak and Coldren, Christopher and Karunamurthy, Arivarasan and Kip, Nefize S. and Klee, Eric W. and Lincoln, Stephen E. and Leon, Annette and Pullambhatla, Mrudula and Temple-Smolkin, Robyn L. and Voelkerding, Karl V. and Wang, Chen and Carter, Alexis B.},
  title={Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines},
  journal={The Journal of Molecular Diagnostics},
  year={2018},
  volume={20},
  pages={4--27},
  month={1},
  doi={10.1016/j.jmoldx.2017.11.003}
}

@article{Schneider2017,
  author={Schneider, Valerie A. and Graves-Lindsay, Tina and Howe, Kerstin and Bouk, Nathan and Chen, Hsiu-Chuan and Kitts, Paul A. and Murphy, Terence D. and Pruitt, Kim D. and Thibaud-Nissen, Fran\c{c}oise and Albracht, Derek and Fulton, Robert S. and Kremitzki, Milinn and Magrini, Vincent and Markovic, Chris and McGrath, Sean and Steinberg, Karyn Meltz and Auger, Kate and Chow, William and Collins, Joanna and Harden, Glenn and Hubbard, Timothy and Pelan, Sarah and Simpson, Jared T. and Threadgold, Glen and Torrance, James and Wood, Jonathan M. and Clarke, Laura and Koren, Sergey and Boitano, Matthew and Peluso, Paul and Li, Heng and Chin, Chen-Shan and Phillippy, Adam M. and Durbin, Richard and Wilson, Richard K. and Flicek, Paul and Eichler, Evan E. and Church, Deanna M.},
  title={Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly},
  journal={Genome Research},
  year={2017},
  volume={27},
  pages={849--864},
  month={5},
  doi={10.1101/gr.213611.116}
}

@article{Garrison2012,
  author={Garrison, Erik and Marth, Gabor},
  title={Haplotype-based variant detection from short-read sequencing},
  year={2012},
  month={Jul}
}

@article{Sorelle2020,
  author={SoRelle, Jeffrey A and Wachsmann, Megan and Cantarel, Brandi L.},
  title={Assembling and Validating Bioinformatic Pipelines for Next-Generation Sequencing Clinical Assays},
  journal={Archives of Pathology \textbackslash{}\& Laboratory Medicine},
  year={2020},
  volume={144},
  pages={1118--1130},
  month={9},
  doi={10.5858/arpa.2019-0476-ra}
}

@article{DeSainteAgathe,
  author={de Sainte Agathe, Jean-Madeleine and Filser, Mathilde and Isidor, Bertrand and Besnard, Thomas and Gueguen, Paul and Perrin, Aur\'{e}lien and Van Goethem, Charles and Verebi, Camille and Masingue, Marion and Rendu, John and Coss\'{e}e, Mireille and Bergougnoux, Anne and Frobert, Laurent and Buratti, Julien and Lejeune, \'{E}lodie and Le Guern, \'{E}ric and Pasquier, Florence and Clot, Fabienne and Kalatzis, Vasiliki and Roux, Anne-Fran\c{c}oise and Cogn\'{e}, Benjamin and Baux, David},
  title={SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation},
  journal={Human Genomics},
  volume={17},
  doi={10.1186/s40246-023-00451-1}
}

@article{Vivian2017,
  author={Vivian, John and Rao, Arjun Arkal and Nothaft, Frank Austin and Ketchum, Christopher and Armstrong, Joel and Novak, Adam and Pfeil, Jacob and Narkizian, Jake and Deran, Alden D and Musselman-Brown, Audrey and Schmidt, Hannes and Amstutz, Peter and Craft, Brian and Goldman, Mary and Rosenbloom, Kate and Cline, Melissa and O'Connor, Brian and Hanna, Megan and Birger, Chet and Kent, W James and Patterson, David A and Joseph, Anthony D and Zhu, Jingchun and Zaranek, Sasha and Getz, Gad and Haussler, David and Paten, Benedict},
  title={Toil enables reproducible, open source, big biomedical data analyses},
  journal={Nature Biotechnology},
  year={2017},
  volume={35},
  pages={314--316},
  month={4},
  doi={10.1038/nbt.3772}
}

@inbook{Ye2018,
  author={Ye, Kai and Guo, Li and Yang, Xiaofei and Lamijer, Eric-Wubbo and Raine, Keiran and Ning, Zemin},
  title={Split-Read Indel and Structural Variant Calling Using PINDEL},
  pages={95--105},
  publisher={Springer New York},
  year={2018},
  month={7},
  doi={10.1007/978-1-4939-8666-8\_7}
}

@article{Koboldt2009,
  author={Koboldt, Daniel C. and Chen, Ken and Wylie, Todd and Larson, David E. and McLellan, Michael D. and Mardis, Elaine R. and Weinstock, George M. and Wilson, Richard K. and Ding, Li},
  title={VarScan: variant detection in massively parallel sequencing of individual and pooled samples},
  journal={Bioinformatics},
  year={2009},
  volume={25},
  pages={2283--2285},
  month={9},
  doi={10.1093/bioinformatics/btp373}
}

@article{Cibulskis2013,
  author={Cibulskis, Kristian and Lawrence, Michael S and Carter, Scott L and Sivachenko, Andrey and Jaffe, David and Sougnez, Carrie and Gabriel, Stacey and Meyerson, Matthew and Lander, Eric S and Getz, Gad},
  title={Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples},
  journal={Nature Biotechnology},
  year={2013},
  volume={31},
  pages={213--219},
  month={3},
  doi={10.1038/nbt.2514}
}

@article{Jarvis2022,
  author={Jarvis, Erich D. and Formenti, Giulio and Rhie, Arang and Guarracino, Andrea and Yang, Chentao and Wood, Jonathan and Tracey, Alan and Thibaud-Nissen, Francoise and Vollger, Mitchell R. and Porubsky, David and Cheng, Haoyu and Asri, Mobin and Logsdon, Glennis A. and Carnevali, Paolo and Chaisson, Mark J. P. and Chin, Chen-Shan and Cody, Sarah and Collins, Joanna and Ebert, Peter and Escalona, Merly and Fedrigo, Olivier and Fulton, Robert S. and Fulton, Lucinda L. and Garg, Shilpa and Gerton, Jennifer L. and Ghurye, Jay and Granat, Anastasiya and Green, Richard E. and Harvey, William and Hasenfeld, Patrick and Hastie, Alex and Haukness, Marina and Jaeger, Erich B. and Jain, Miten and Kirsche, Melanie and Kolmogorov, Mikhail and Korbel, Jan O. and Koren, Sergey and Korlach, Jonas and Lee, Joyce and Li, Daofeng and Lindsay, Tina and Lucas, Julian and Luo, Feng and Marschall, Tobias and Mitchell, Matthew W. and McDaniel, Jennifer and Nie, Fan and Olsen, Hugh E. and Olson, Nathan D. and Pesout, Trevor and Potapova, Tamara and Puiu, Daniela and Regier, Allison and Ruan, Jue and Salzberg, Steven L. and Sanders, Ashley D. and Schatz, Michael C. and Schmitt, Anthony and Schneider, Valerie A. and Selvaraj, Siddarth and Shafin, Kishwar and Shumate, Alaina and Stitziel, Nathan O. and Stober, Catherine and Torrance, James and Wagner, Justin and Wang, Jianxin and Wenger, Aaron and Xiao, Chuanle and Zimin, Aleksey V. and Zhang, Guojie and Wang, Ting and Li, Heng and Garrison, Erik and Haussler, David and Hall, Ira and Zook, Justin M. and Eichler, Evan E. and Phillippy, Adam M. and Paten, Benedict and Howe, Kerstin and Miga, Karen H. and None, None},
  title={Semi-automated assembly of high-quality diploid human reference genomes},
  journal={Nature},
  year={2022},
  volume={611},
  pages={519--531},
  month={11},
  doi={10.1038/s41586-022-05325-5}
}

@article{Rhie2023,
  author={Rhie, Arang and Nurk, Sergey and Cechova, Monika and Hoyt, Savannah J. and Taylor, Dylan J. and Altemose, Nicolas and Hook, Paul W. and Koren, Sergey and Rautiainen, Mikko and Alexandrov, Ivan A. and Allen, Jamie and Asri, Mobin and Bzikadze, Andrey V. and Chen, Nae-Chyun and Chin, Chen-Shan and Diekhans, Mark and Flicek, Paul and Formenti, Giulio and Fungtammasan, Arkarachai and Garcia Giron, Carlos and Garrison, Erik and Gershman, Ariel and Gerton, Jennifer L. and Grady, Patrick G. S. and Guarracino, Andrea and Haggerty, Leanne and Halabian, Reza and Hansen, Nancy F. and Harris, Robert and Hartley, Gabrielle A. and Harvey, William T. and Haukness, Marina and Heinz, Jakob and Hourlier, Thibaut and Hubley, Robert M. and Hunt, Sarah E. and Hwang, Stephen and Jain, Miten and Kesharwani, Rupesh K. and Lewis, Alexandra P. and Li, Heng and Logsdon, Glennis A. and Lucas, Julian K. and Makalowski, Wojciech and Markovic, Christopher and Martin, Fergal J. and Mc Cartney, Ann M. and McCoy, Rajiv C. and McDaniel, Jennifer and McNulty, Brandy M. and Medvedev, Paul and Mikheenko, Alla and Munson, Katherine M. and Murphy, Terence D. and Olsen, Hugh E. and Olson, Nathan D. and Paulin, Luis F. and Porubsky, David and Potapova, Tamara and Ryabov, Fedor and Salzberg, Steven L. and Sauria, Michael E. G. and Sedlazeck, Fritz J. and Shafin, Kishwar and Shepelev, Valery A. and Shumate, Alaina and Storer, Jessica M. and Surapaneni, Likhitha and Taravella Oill, Angela M. and Thibaud-Nissen, Fran\c{c}oise and Timp, Winston and Tomaszkiewicz, Marta and Vollger, Mitchell R. and Walenz, Brian P. and Watwood, Allison C. and Weissensteiner, Matthias H. and Wenger, Aaron M. and Wilson, Melissa A. and Zarate, Samantha and Zhu, Yiming and Zook, Justin M. and Eichler, Evan E. and O'Neill, Rachel J. and Schatz, Michael C. and Miga, Karen H. and Makova, Kateryna D. and Phillippy, Adam M.},
  title={The complete sequence of a human Y chromosome},
  journal={Nature},
  year={2023},
  volume={621},
  pages={344--354},
  month={9},
  doi={10.1038/s41586-023-06457-y}
}

@article{Mclaren,
  author={McLaren, William and Gil, Laurent and Hunt, Sarah E. and Riat, Harpreet Singh and Ritchie, Graham R. S. and Thormann, Anja and Flicek, Paul and Cunningham, Fiona},
  title={The Ensembl Variant Effect Predictor},
  journal={Genome Biology},
  volume={17},
  doi={10.1186/s13059-016-0974-4}
}

@article{Pruitt,
  author={Pruitt, Kim D. and Brown, Garth R. and Hiatt, Susan M. and Thibaud-Nissen, Fran\c{c}oise and Astashyn, Alexander and Ermolaeva, Olga and Farrell, Catherine M. and Hart, Jennifer and Landrum, Melissa J. and McGarvey, Kelly M. and Murphy, Michael R. and O'Leary, Nuala A. and Pujar, Shashikant and Rajput, Bhanu and Rangwala, Sanjida H. and Riddick, Lillian D. and Shkeda, Andrei and Sun, Hanzhen and Tamez, Pamela and Tully, Raymond E. and Wallin, Craig and Webb, David and Weber, Janet and Wu, Wendy and DiCuccio, Michael and Kitts, Paul and Maglott, Donna R. and Murphy, Terence D. and Ostell, James M.},
  title={RefSeq: an update on mammalian reference sequences},
  journal={Nucleic Acids Research},
  volume={42},
  doi={10.1093/nar/gkt1114}
}

@article{Hardwick2017,
  author={Hardwick, Simon A. and Deveson, Ira W. and Mercer, Tim R.},
  title={Reference standards for next-generation sequencing},
  journal={Nature Reviews Genetics},
  year={2017},
  volume={18},
  pages={473--484},
  month={8},
  doi={10.1038/nrg.2017.44}
}

@article{Danecek2021,
  author={Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
  title={Twelve years of SAMtools and BCFtools},
  journal={GigaScience},
  year={2021},
  volume={10},
  month={1},
  doi={10.1093/gigascience/giab008}
}

@article{Miller2021,
  author={Miller, Thiago L A and Orpinelli Rego, Fernanda and Buzzo, Jos\'{e} Leonel L and Galante, Pedro A F},
  title={sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies},
  journal={Bioinformatics},
  year={2021},
  volume={37},
  pages={419--421},
  month={4},
  doi={10.1093/bioinformatics/btaa689}
}

@misc{Olson2020,
  author={Olson, Nathan D. and Wagner, Justin and McDaniel, Jennifer and Stephens, Sarah H. and Westreich, Samuel T. and Prasanna, Anish G. and Johanson, Elaine and Boja, Emily and Maier, Ezekiel J. and Serang, Omar and J\'{a}spez, David and Lorenzo-Salazar, Jos\'{e} M. and Mu\ {n}oz-Barrera, Adri\'{a}n and Rubio-Rodr\'{\i}guez, Luis A. and Flores, Carlos and Kyriakidis, Konstantinos and Malousi, Andigoni and Shafin, Kishwar and Pesout, Trevor and Jain, Miten and Paten, Benedict and Chang, Pi-Chuan and Kolesnikov, Alexey and Nattestad, Maria and Baid, Gunjan and Goel, Sidharth and Yang, Howard and Carroll, Andrew and Eveleigh, Robert and Bourgey, Mathieu and Bourque, Guillaume and Li, Gen and ChouXian, MA and Tang, LinQi and YuanPing, DU and Zhang, ShaoWei and Morata, Jordi and Tonda, Ra\'{u}l and Parra, Gen\'{\i}s and Trotta, Jean-R\'{e}mi and Brueffer, Christian and Demirkaya-Budak, Sinem and Kabakci-Zorlu, Duygu and Turgut, Deniz and Kalay, \"{O}zem and Budak, Gungor and Narc\i{}, K\"{u}bra and Arslan, Elif and Brown, Richard and Johnson, Ivan J and Dolgoborodov, Alexey and Semenyuk, Vladimir and Jain, Amit and Tetikol, H. Serhat and Jain, Varun and Ruehle, Mike and Lajoie, Bryan and Roddey, Cooper and Catreux, Severine and Mehio, Rami and Ahsan, Mian Umair and Liu, Qian and Wang, Kai and Sahraeian, Sayed Mohammad Ebrahim and Fang, Li Tai and Mohiyuddin, Marghoob and Hung, Calvin and Jain, Chirag and Feng, Hanying and Li, Zhipan and Chen, Luoqi and Sedlazeck, Fritz J. and Zook, Justin M.},
  title={precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions},
  month={11},
  year={2020},
  doi={10.1101/2020.11.13.380741},
  url={http://dx.doi.org/10.1101/2020.11.13.380741}
}

@article{Zook2014,
  author={Zook, Justin M and Chapman, Brad and Wang, Jason and Mittelman, David and Hofmann, Oliver and Hide, Winston and Salit, Marc},
  title={Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls},
  journal={Nature Biotechnology},
  year={2014},
  volume={32},
  pages={246--251},
  month={3},
  doi={10.1038/nbt.2835}
}

@article{Aganezov2022,
  author={Aganezov, Sergey and Yan, Stephanie M. and Soto, Daniela C. and Kirsche, Melanie and Zarate, Samantha and Avdeyev, Pavel and Taylor, Dylan J. and Shafin, Kishwar and Shumate, Alaina and Xiao, Chunlin and Wagner, Justin and McDaniel, Jennifer and Olson, Nathan D. and Sauria, Michael E. G. and Vollger, Mitchell R. and Rhie, Arang and Meredith, Melissa and Martin, Skylar and Lee, Joyce and Koren, Sergey and Rosenfeld, Jeffrey A. and Paten, Benedict and Layer, Ryan and Chin, Chen-Shan and Sedlazeck, Fritz J. and Hansen, Nancy F. and Miller, Danny E. and Phillippy, Adam M. and Miga, Karen H. and McCoy, Rajiv C. and Dennis, Megan Y. and Zook, Justin M. and Schatz, Michael C.},
  title={A complete reference genome improves analysis of human genetic variation},
  journal={Science},
  year={2022},
  volume={376},
  month={4},
  doi={10.1126/science.abl3533}
}

@inbook{Dolstra2004,
  author={Eelco Dolstra and Merijn de Jonge and Eelco Visser},
  title={Nix: A Safe and Policy-Free System for Software Deployment},
  year={2004}
}

@misc{Baid2020,
  author={Baid, Gunjan and Nattestad, Maria and Kolesnikov, Alexey and Goel, Sidharth and Yang, Howard and Chang, Pi-Chuan and Carroll, Andrew},
  title={An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development},
  month={12},
  year={2020},
  doi={10.1101/2020.12.11.422022},
  url={http://dx.doi.org/10.1101/2020.12.11.422022}
}

@article{Krusche2019,
  author={Krusche, Peter and None, None and Trigg, Len and Boutros, Paul C. and Mason, Christopher E. and De La Vega, Francisco M. and Moore, Benjamin L. and Gonzalez-Porta, Mar and Eberle, Michael A. and Tezak, Zivana and Lababidi, Samir and Truty, Rebecca and Asimenos, George and Funke, Birgit and Fleharty, Mark and Chapman, Brad A. and Salit, Marc and Zook, Justin M.},
  title={Best practices for benchmarking germline small-variant calls in human genomes},
  journal={Nature Biotechnology},
  year={2019},
  volume={37},
  pages={555--560},
  month={5},
  doi={10.1038/s41587-019-0054-x}
}

@article{Wang,
  author={Wang, Kai and Li, Mingyao and Hakonarson, Hakon},
  title={ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data},
  journal={Nucleic Acids Research},
  year={2010},
  volume={38},
  doi={10.1093/nar/gkq603}
}

@article{Pei2021,
  author={Pei, Surui and Liu, Tao and Ren, Xue and Li, Weizhong and Chen, Chongjian and Xie, Zhi},
  title={Benchmarking variant callers in next-generation and third-generation sequencing analysis},
  journal={Briefings in Bioinformatics},
  year={2021},
  volume={22},
  month={5},
  doi={10.1093/bib/bbaa148}
}

@article{Sherry2001,
  author={Sherry, S. T.},
  title={dbSNP: the NCBI database of genetic variation},
  journal={Nucleic Acids Research},
  year={2001},
  volume={29},
  pages={308--311},
  month={1},
  doi={10.1093/nar/29.1.308}
}

@article{Cameron2021,
  author={Cameron, Daniel L. and Baber, Jonathan and Shale, Charles and Valle-Inclan, Jose Espejo and Besselink, Nicolle and van Hoeck, Arne and Janssen, Roel and Cuppen, Edwin and Priestley, Peter and Papenfuss, Anthony T.},
  title={GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing},
  journal={Genome Biology},
  year={2021},
  volume={22},
  month={12},
  doi={10.1186/s13059-021-02423-x}
}

@article{Wilcox2021,
  author={Wilcox, Emma and Harrison, Steven M. and Lockhart, Edward and Voelkerding, Karl and Lubin, Ira M. and Rehm, Heidi L. and Kalman, Lisa V. and Funke, Birgit},
  title={Creation of an Expert Curated Variant List for Clinical Genomic Test Development and Validation},
  journal={The Journal of Molecular Diagnostics},
  year={2021},
  volume={23},
  pages={1500--1505},
  month={11},
  doi={10.1016/j.jmoldx.2021.07.018}
}

@article{Rausch2012,
  author={Rausch, Tobias and Zichner, Thomas and Schlattl, Andreas and St\"{u}tz, Adrian M. and Benes, Vladimir and Korbel, Jan O.},
  title={DELLY: structural variant discovery by integrated paired-end and split-read analysis},
  journal={Bioinformatics},
  year={2012},
  volume={28},
  pages={i333--i339},
  month={9},
  doi={10.1093/bioinformatics/bts378}
}

@article{Peyrard2008,
  author={Peyrard, T. and Pham, B.-N. and Le Pennec, P.-Y. and Rouger, P.},
  title={Les ph\'{e}notypes \'{e}rythrocytaires rares : un enjeu de sant\'{e} publique},
  journal={Transfusion Clinique et Biologique},
  year={2008},
  volume={15},
  pages={109--119},
  month={6},
  doi={10.1016/j.tracli.2008.02.001}
}

@article{Zeng2022,
  author={Zeng, Tony and Li, Yang I},
  title={Predicting RNA splicing from DNA sequence using Pangolin},
  journal={Genome Biology},
  year={2022},
  volume={23},
  doi={10.1186/s13059-022-02664-4}
}

@article{VanDerAuwera2013,
  author={Van der Auwera, Geraldine A. and Carneiro, Mauricio O. and Hartl, Christopher and Poplin, Ryan and del Angel, Guillermo and Levy-Moonshine, Ami and Jordan, Tadeusz and Shakir, Khalid and Roazen, David and Thibault, Joel and Banks, Eric and Garimella, Kiran V. and Altshuler, David and Gabriel, Stacey and DePristo, Mark A.},
  title={From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline},
  journal={Current Protocols in Bioinformatics},
  year={2013},
  volume={43},
  month={10},
  doi={10.1002/0471250953.bi1110s43}
}

@article{Landrum2016,
  author={Landrum, Melissa J. and Lee, Jennifer M. and Benson, Mark and Brown, Garth and Chao, Chen and Chitipiralla, Shanmuga and Gu, Baoshan and Hart, Jennifer and Hoffman, Douglas and Hoover, Jeffrey and Jang, Wonhee and Katz, Kenneth and Ovetsky, Michael and Riley, George and Sethi, Amanjeev and Tully, Ray and Villamarin-Salomon, Ricardo and Rubinstein, Wendy and Maglott, Donna R.},
  title={ClinVar: public archive of interpretations of clinically relevant variants},
  journal={Nucleic Acids Research},
  year={2016},
  volume={44},
  pages={D862--D868},
  month={1},
  doi={10.1093/nar/gkv1222}
}

@article{CofracSHGTA16,
  author={COFRAC},
  title={Guide technique d\textbackslash{}'accr\'{e}ditation de la technologie de s\'{e}quen\c{c}age \`{a} haut d\'{e}bit},
  year={2019}
}

@article{Barbitoff2022,
  author={Barbitoff, Yury A. and Abasov, Ruslan and Tvorogova, Varvara E. and Glotov, Andrey S. and Predeus, Alexander V.},
  title={Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery},
  journal={BMC Genomics},
  year={2022},
  volume={23},
  month={12},
  doi={10.1186/s12864-022-08365-3}
}

@article{Kumaran2019,
  author={Kumaran, Manojkumar and Subramanian, Umadevi and Devarajan, Bharanidharan},
  title={Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data},
  journal={BMC Bioinformatics},
  year={2019},
  volume={20},
  month={12},
  doi={10.1186/s12859-019-2928-9}
}

@article{Hatem2013,
  author={Hatem, Ayat and Bozda\u{g}, Doruk and Toland, Amanda E and \c{C}ataly\"{u}rek, \"{U}mit V},
  title={Benchmarking short sequence mapping tools},
  journal={BMC Bioinformatics},
  year={2013},
  volume={14},
  month={12},
  doi={10.1186/1471-2105-14-184}
}

@article{Jakobsen2019,
  author={Jakobsen, M. A. and Dellgren, C. and Sheppard, C. and Yazer, M. and Sprog\o{}e, U.},
  title={The use of next-generation sequencing for the determination of rare blood group genotypes},
  journal={Transfusion Medicine},
  year={2019},
  volume={29},
  pages={162--168},
  month={6},
  doi={10.1111/tme.12496}
}

@article{Nurk2022,
  author={Nurk, Sergey and Koren, Sergey and Rhie, Arang and Rautiainen, Mikko and Bzikadze, Andrey V. and Mikheenko, Alla and Vollger, Mitchell R. and Altemose, Nicolas and Uralsky, Lev and Gershman, Ariel and Aganezov, Sergey and Hoyt, Savannah J. and Diekhans, Mark and Logsdon, Glennis A. and Alonge, Michael and Antonarakis, Stylianos E. and Borchers, Matthew and Bouffard, Gerard G. and Brooks, Shelise Y. and Caldas, Gina V. and Chen, Nae-Chyun and Cheng, Haoyu and Chin, Chen-Shan and Chow, William and de Lima, Leonardo G. and Dishuck, Philip C. and Durbin, Richard and Dvorkina, Tatiana and Fiddes, Ian T. and Formenti, Giulio and Fulton, Robert S. and Fungtammasan, Arkarachai and Garrison, Erik and Grady, Patrick G. S. and Graves-Lindsay, Tina A. and Hall, Ira M. and Hansen, Nancy F. and Hartley, Gabrielle A. and Haukness, Marina and Howe, Kerstin and Hunkapiller, Michael W. and Jain, Chirag and Jain, Miten and Jarvis, Erich D. and Kerpedjiev, Peter and Kirsche, Melanie and Kolmogorov, Mikhail and Korlach, Jonas and Kremitzki, Milinn and Li, Heng and Maduro, Valerie V. and Marschall, Tobias and McCartney, Ann M. and McDaniel, Jennifer and Miller, Danny E. and Mullikin, James C. and Myers, Eugene W. and Olson, Nathan D. and Paten, Benedict and Peluso, Paul and Pevzner, Pavel A. and Porubsky, David and Potapova, Tamara and Rogaev, Evgeny I. and Rosenfeld, Jeffrey A. and Salzberg, Steven L. and Schneider, Valerie A. and Sedlazeck, Fritz J. and Shafin, Kishwar and Shew, Colin J. and Shumate, Alaina and Sims, Ying and Smit, Arian F. A. and Soto, Daniela C. and Sovi\'{c}, Ivan and Storer, Jessica M. and Streets, Aaron and Sullivan, Beth A. and Thibaud-Nissen, Fran\c{c}oise and Torrance, James and Wagner, Justin and Walenz, Brian P. and Wenger, Aaron and Wood, Jonathan M. D. and Xiao, Chunlin and Yan, Stephanie M. and Young, Alice C. and Zarate, Samantha and Surti, Urvashi and McCoy, Rajiv C. and Dennis, Megan Y. and Alexandrov, Ivan A. and Gerton, Jennifer L. and O'Neill, Rachel J. and Timp, Winston and Zook, Justin M. and Schatz, Michael C. and Eichler, Evan E. and Miga, Karen H. and Phillippy, Adam M.},
  title={The complete sequence of a human genome},
  journal={Science},
  year={2022},
  volume={376},
  pages={44--53},
  month={4},
  doi={10.1126/science.abj6987}
}

@article{Yen2017,
  author={Yen, Jennifer L. and Garcia, Sarah and Montana, Aldrin and Harris, Jason and Chervitz, Stephen and Morra, Massimo and West, John and Chen, Richard and Church, Deanna M.},
  title={A variant by any name: quantifying annotation discordance across tools and clinical databases},
  journal={Genome Medicine},
  year={2017},
  volume={9},
  doi={10.1186/s13073-016-0396-7}
}

@article{Vallet2022,
  author={Vallet, Nicolas and Michonneau, David and Tournier, Simon},
  title={Toward practical transparent verifiable and long-term reproducible research using Guix},
  journal={Scientific Data},
  year={2022},
  volume={9},
  month={10},
  doi={10.1038/s41597-022-01720-9}
}

@article{Alser2021,
  author={Alser, Mohammed and Rotman, Jeremy and Deshpande, Dhrithi and Taraszka, Kodi and Shi, Huwenbo and Baykal, Pelin Icer and Yang, Harry Taegyun and Xue, Victor and Knyazev, Sergey and Singer, Benjamin D. and Balliu, Brunilda and Koslicki, David and Skums, Pavel and Zelikovsky, Alex and Alkan, Can and Mutlu, Onur and Mangul, Serghei},
  title={Technology dictates algorithms: recent developments in read alignment},
  journal={Genome Biology},
  year={2021},
  volume={22},
  month={12},
  doi={10.1186/s13059-021-02443-7}
}

@article{ngsdiag2019,
  author={NGS-Diag},
  title={Qualification des solution bioinformatiques: note technique},
  year={2019}
}

@article{Li2009,
  author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and None, None},
  title={The Sequence Alignment/Map format and SAMtools},
  journal={Bioinformatics},
  year={2009},
  volume={25},
  pages={2078--2079},
  month={8},
  doi={10.1093/bioinformatics/btp352}
}

@article{Kuchel,
  author={Kuchel, Philip W. and Cox, Charles D. and Daners, Daniel and Shishmarev, Dmitry and Galvosas, Petrik},
  title={Surface model of the human red blood cell simulating changes in membrane curvature under strain},
  journal={Scientific Reports},
  volume={11},
  doi={10.1038/s41598-021-92699-7}
}