Evaluating the performance of tools used to call minority variants from whole genome short-read data.

ABSTRACT: Background: High-throughput whole genome sequencing facilitates investigation of minority virus sub-populations from virus positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics and can potentially assist in elucidating person-person transmission pathways. Several minority variant callers have been developed to describe low frequency sub-populations from whole genome sequence data. These callers differ based on bioinformatics and statistical methods used to discriminate sequencing errors from low-frequency variants. Methods: We evaluated the diagnostic performance and concordance between published minority variant callers used in identifying minority variants from whole-genome sequence data from virus samples. We

SUBMITTER: Said Mohammed K 

PROVIDER: S-EPMC6234735 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature