Scaling accurate genetic variant discovery to tens of thousands of samples
Ryan E. Poplin, Valentín Ruano-Rubio, Mark A. DePristo, Tim J. Fennell, Mauricio O. Carneiro, Geraldine A. Van der Auwera, David E. Kling, Laura Doyle Gauthier, Ami Levy‐Moonshine, David Roazen, Khalid Shakir, Joel Thibault, Sheila Chandran, Chris Whelan, Monkol Lek, , Eric Banks
Per-sample assembly with gVCF output, followed by joint genotyping, lets GATK HaplotypeCaller scale linearly with cohort size while calling indels more accurately than SAMtools, UnifiedGenotyper or Platypus.
bioRxiv · Jul 24, 2018 · PreprintGenomics✦ In-depth digest