Accurate, scalable cohort variant calls using DeepVariant and GLnexus.

ABSTRACT:

Motivation

Population-scale sequenced cohorts are foundational resources for genetic analyses, but processing raw reads into analysis-ready cohort-level variants remains challenging.

Results

We introduce an open-source cohort-calling method that uses the highly accurate caller DeepVariant and scalable merging tool GLnexus. Using callset quality metrics based on variant recall and precision in benchmark samples and Mendelian consistency in father-mother-child trios, we optimize the method across a range of cohort sizes, sequencing methods and sequencing depths. The resulting callsets show consistent quality improvements over those generated using existing best practices with reduced cost. We further evaluate our pipeline in the deeply sequenced 1000 Genomes Project (1KGP) sam

SUBMITTER: Yun T 

PROVIDER: S-EPMC8023681 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature