CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing.

ABSTRACT: Next-generation sequencing (NGS) has revolutionized genetics and enabled the accurate identification of many genetic variants across many genomes. However, detection of biologically important low-frequency variants within genetically heterogeneous populations remains challenging, because they are difficult to distinguish from intrinsic NGS sequencing error rates. Approaches to overcome these limitations are essential to detect rare mutations in large cohorts, virus or microbial populations, mitochondria heteroplasmy, and other heterogeneous mixtures such as tumors. Modifications in library preparation can overcome some of these limitations, but are experimentally challenging and restricted to skilled biologists. This paper describes a novel quality filtering and base pruning pipeline, call

SUBMITTER: Salehi F 

PROVIDER: S-EPMC4333345 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature