SmCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.

ABSTRACT:

Motivation

Low-frequency DNA mutations are often confounded with technical artifacts from sample preparation and sequencing. With unique molecular identifiers (UMIs), most of the sequencing errors can be corrected. However, errors before UMI tagging, such as DNA polymerase errors during end repair and the first PCR cycle, cannot be corrected with single-strand UMIs and impose fundamental limits to UMI-based variant calling.

Results

We developed smCounter2, a UMI-based variant caller for targeted sequencing data and an upgrade from the current version of smCounter. Compared to smCounter, smCounter2 features lower detection limit that decreases from 1 to 0.5%, better overall accuracy (particularly in non-coding regions), a consistent threshold that can be applied to both deep

SUBMITTER: Xu C 

PROVIDER: S-EPMC6477992 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature