Assessing reproducibility of inherited variants detected with short-read whole genome sequencing.

ABSTRACT:

Background

Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS.

Results

To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligner

SUBMITTER: Pan B 

PROVIDER: S-EPMC8722114 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature