BCFtools/csq: haplotype-aware variant consequences.

ABSTRACT:

Motivation

Prediction of functional variant consequences is an important part of sequencing pipelines, allowing the categorization and prioritization of genetic variants for follow up analysis. However, current predictors analyze variants as isolated events, which can lead to incorrect predictions when adjacent variants alter the same codon, or when a frame-shifting indel is followed by a frame-restoring indel. Exploiting known haplotype information when making consequence predictions can resolve these issues.

Results

BCFtools/csq is a fast program for haplotype-aware consequence calling which can take into account known phase. Consequence predictions are changed for 501 of 5019 compound variants found in the 81.7M variants in the 1000 Genomes Project data, with an average o

SUBMITTER: Danecek P 

PROVIDER: S-EPMC5870570 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature