Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects.

ABSTRACT: Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power. A central challenge for joint analysis is that different WGS data processing pipelines cause substantial differences in variant calling in combined datasets, necessitating computationally expensive reprocessing. This approach is no longer tenable given the scale of current studies and data volumes. Here, we define WGS data processing standards that allow different groups to produce functionally equivalent (FE) results, yet still innovate on data processing pipelines. We present initial FE pipelines developed at five genome centers and show that they

SUBMITTER: Regier AA 

PROVIDER: S-EPMC6168605 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature