* Inspiration
:PROPERTIES:
:CUSTOM_ID: inspiration
:END:
** Bcbio
:PROPERTIES:
:CUSTOM_ID: bcbio
:END:
Schémas de validation par la communauté:
https://github.com/bcbio/bcbio_validation_workflows - GIAB: Les génomes
sont restreints aux exomes - NA12878: (Caucasian daughter): 65x NovaSeq
TruSeq Nano - NA24385 (Ashkenazi Jewish son): 50x HiSeq x10 dataset from
10x genomics - NA24631 ( - GIAB exomes - NA12878 exome -- From Illumina
Basespace Public datasets, 200x NovaSeq S2 using the Illumina TruSeq DNA
Library Prep for Enrichment with IDT xGen Exome Research Panel v1.0,
trimmed to 2x101 for analysis. - NA24385 exome -- from Oslo University
Hospital's contribution to the Genome in a Bottle Project: 150x Illumina
HiSeq 2500 with 150bp paired-end reads, Agilent SureSelect Human All
Exon V5 kit - NA24631 exome -- also from Oslo University Hospital's GiaB
contribution, 100x Illumina HiSeq 2500 sequencing. - CHM : Les génomes
sont restreints aux exomes - structural variant - somatic

** Autre
:PROPERTIES:
:CUSTOM_ID: autre
:END:
Méthodologie
https://medium.com/dnanexus/benchmarking-state-of-the-art-secondary-variant-calling-pipelines-5472ca6bace7

#+begin_example
We downloaded raw HG001 WES reads from NIST FTP site with ~141X on-target coverage. 
Raw WES reads for HG002, HG003, HG004, and HG005 were downloaded from the SRA study, SRP047086
#+end_example

https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=study&acc=SRP047086
On a 1 exome pour HG002-HHG004 sur Illumina HiSeq 2500 avec Agilent
SureSelect Human All Exon V5 kit. Ce sont les fichiers disponibles sur
le FTP GIAB mais les fastq sont directement accessible sur ENA en avec
ces références !
https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP047086&f=assay_type_s%3An%3Awxs%3Ac&o=acc_s%3Aa

https://zenodo.org/records/3597727