Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data.

ABSTRACT: The emergence of next-generation sequencing (NGS) has revolutionized the way of reaching a genome sequence, with the promise of potentially providing a comprehensive characterization of DNA variations. Nevertheless, detecting somatic mutations is still a difficult problem, in particular when trying to identify low abundance mutations, such as subclonal mutations, tumour-derived alterations in body fluids or somatic mutations from histological normal tissue. The main challenge is to precisely distinguish between sequencing artefacts and true mutations, particularly when the latter are so rare they reach similar abundance levels as artefacts. Here, we present needlestack, a highly sensitive variant caller, which directly learns from the data the level of systematic sequencing errors to accur

SUBMITTER: Delhomme TM 

PROVIDER: S-EPMC7182099 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature