BCFtools/csq: haplotype-aware variant consequences

By Petr Danecek, Shane A. McCarthy. bioRxiv, 2016

408 citations recorded by the source corpus.

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 of 139 compound variants per haplotype. Predictions match existing tools when run in localized mode, but the program is an order of magnitude faster and requires an order of magnitude less memory. Availability: The program is freely available for commercial and non-commercial use in the BCFtools package which is available for download from http://samtools.github.io/bcftools Contact: pd3@sanger.ac.uk

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/35cddad6993f5c31d7e784d4207cbcbd1bee34eb

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Citations in the corpus

Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes (2020, background): “For the methylation data, we collected the genome methylation level from ENCODE, and calculated the fraction of methylated CpG out of all the CpGs in the region, and ordered by the fraction (Supplementary Table 4).”