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Bioinformatics. 2017 May 15;33(10):1581-1582. doi: 10.1093/bioinformatics/btx011.

VCF-kit: assorted utilities for the variant call format.

Author information

1
Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA.
2
Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.

Abstract

Summary:

The variant call format (VCF) is a popular standard for storing genetic variation data. As a result, a large collection of tools has been developed that perform diverse analyses using VCF files. However, some tasks common to statistical and population geneticists have not been created yet. To streamline these types of analyses, we created novel tools that analyze or annotate VCF files and organized these tools into a command-line based utility named VCF-kit. VCF-kit adds essential utilities to process and analyze VCF files, including primer generation for variant validation, dendrogram production, genotype imputation from sequence data in linkage studies, and additional tools.

Availability and Implementation:

https://github.com/AndersenLab/VCF-kit.

Contact:

erik.andersen@northwestern.edu.

PMID:
28093408
PMCID:
PMC5423453
DOI:
10.1093/bioinformatics/btx011
[Indexed for MEDLINE]
Free PMC Article

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