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Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5.

Vcfanno: fast, flexible annotation of genetic variants.

Pedersen BS1,2,3, Layer RM4,5,6, Quinlan AR7,8,9.

Author information

1
Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA. bpederse@gmail.com.
2
USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84105, USA. bpederse@gmail.com.
3
Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84105, USA. bpederse@gmail.com.
4
Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA.
5
USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84105, USA.
6
Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84105, USA.
7
Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA. aquinlan@genetics.utah.edu.
8
USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, 84105, USA. aquinlan@genetics.utah.edu.
9
Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84105, USA. aquinlan@genetics.utah.edu.

Abstract

The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel "chromosome sweeping" algorithm, we demonstrate substantial performance gains by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license.

KEYWORDS:

Annotation; Genetic variation; Genome analysis; SNP; VCF; Variant; Variant prioritization

PMID:
27250555
PMCID:
PMC4888505
DOI:
10.1186/s13059-016-0973-5
[Indexed for MEDLINE]
Free PMC Article

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