*** Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers
Comparaison de différents pipeline 2019
https://www.nature.com/articles/s41598-019-45835-3
Combinaison
- variant calling = GATK, Strelka2 and Samtools-Varscan2
- sur NA12878
- séquencé sur BGISEQ500, MGISEQ2000, HiSeq4000, NovaSeq and HiSeq Xten.
Conclusion: strelka2 supérieur mais biais sur NA12878 ?
Illumina > BGI pour indel, probablement car reads plus grand
#+begin_quote
For WES datasets, the BGI platforms displayed the superior performance in SNPs
calling while Illumina platforms manifested the better variants calling
performance in INDELs calling, which could be explained by their divergence in
sequencing strategy that producing different length of reads (all BGI platforms
were 100 base pair read length while all Illumina platforms were 150 base pair
read length). The read length effects, as a key factor between two platforms,
would bring alignment bias and error which are higher for short reads and
ultimately affect the variants calling especially the INDELs identification
#+end_quote