A thesaurus of genetic variation for interrogation of repetitive genomic regions.

ABSTRACT: Detecting genetic variation is one of the main applications of high-throughput sequencing, but is still challenging wherever aligning short reads poses ambiguities. Current state-of-the-art variant calling approaches avoid such regions, arguing that it is necessary to sacrifice detection sensitivity to limit false discovery. We developed a method that links candidate variant positions within repetitive genomic regions into clusters. The technique relies on a resource, a thesaurus of genetic variation, that enumerates genomic regions with similar sequence. The resource is computationally intensive to generate, but once compiled can be applied efficiently to annotate and prioritize variants in repetitive regions. We show that thesaurus annotation can reduce the rate of false variant calls du

SUBMITTER: Kerzendorfer C 

PROVIDER: S-EPMC4446415 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature