ReliableGenome: annotation of genomic regions with high/low variant calling concordance.

ABSTRACT:

Motivation

The increasing adoption of clinical whole-genome resequencing (WGS) demands for highly accurate and reproducible variant calling (VC) methods. The observed discordance between state-of-the-art VC pipelines, however, indicates that the current practice still suffers from non-negligible numbers of false positive and negative SNV and INDEL calls that were shown to be enriched among discordant calls but also in genomic regions with low sequence complexity.

Results

Here, we describe our method ReliableGenome (RG) for partitioning genomes into high and low concordance regions with respect to a set of surveyed VC pipelines. Our method combines call sets derived by multiple pipelines from arbitrary numbers of datasets and interpolates expected concordance for genomic regi

SUBMITTER: Popitsch N 

PROVIDER: S-EPMC5903559 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature