VCFtools protocols

VCFtools specifications


Unique identifier OMICS_02105
Name VCFtools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF
Output format VCF
Operating system Unix/Linux
Programming languages C++, Perl
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Richard Durbin <>

Additional information

Publication for VCFtools

VCFtools IN pipelines

PMCID: 5776132
PMID: 29387076
DOI: 10.3389/fpls.2017.02269

[…] 2013) by bwa (li and durbin, 2009). then snp/indel variants were called using gatk (mckenna et al., 2010; depristo et al., 2011). finally, snp/indel density was calculated from the variation data by vcftools (danecek et al., 2011)., to verify the indel variants derived from resequencing analysis, we designed specific pcr primers for randomly selected indel variants with 3bp or more difference, […]

PMCID: 5785814
PMID: 29370772
DOI: 10.1186/s12864-018-4444-0

[…] the genome-wide genetic differentiation between broiler and layer lines. chromosomes w/z, unplaced, random, and mitochondrial were not considered in this study. this method was performed using vcftools v. 0.1.12 software [69] with snp (n = 12,806,643) and indel (n = 1,273,210) datasets considered separately and using overlapping windows of 20 kb and a step size of 10 kb. weighted fst […]

PMCID: 5805289
PMID: 29420653
DOI: 10.1371/journal.pone.0192446

[…] to find the populations wise genetic differentiation with respect to cardiovascular diseases, pair-wise weir and cockerham fst [43] values were calculated for the 1000 genomes data, using the vcftools. for this purpose, two approaches were employed, i.e fst calculation for all the genes which harbored the predicted deleterious snvs in this analysis, and for deleterious snvs […]

PMCID: 5826192
PMID: 29515573
DOI: 10.3389/fimmu.2018.00242

[…] lankan tamil (stu), and telugu (itu). all known snps annotated by the 1000 genomes project were retrieved as vcf files and filtered for the amplicon regions covered in our ampliseq approach using vcftools (52) and for a maf > 0.05 using the genomeanalysistoolkit (gatk v. 3.2) (53, 54). the filtered snp list was then pruned using plink (55) in order to exclude less informative snps […]

PMCID: 5836840
PMID: 29504900
DOI: 10.1186/s12920-018-0326-1

[…] depth based on trusight one sequencing panel target region list. the raw sequencing data have been processed with a custom pipeline based on popular open-source bioinformatics tools bwa, samtools, vcftools, as well as in-house perl scripts, using hg19 assembly as a reference sequence. in total 49,772 nucleotide variants were found. variant annotations were added by snpeff/snpsift software […]

VCFtools institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Boston College, MA, USA; National Institutes of Health National Center for Biotechnology Information, MD, USA; Department of Statistics, University of Oxford, Oxford, UK
VCFtools funding source(s)
Supported by Medical Research Council, UK; British Heart Foundation (grant RG/09/012/28096); Wellcome Trust (grants 090532/Z/09/Z and 075491/Z/04); National Human Genome Research Institute (grants 54 HG003067, R01 HG004719 and U01 HG005208); Intramural Research Program of the National Institutes of Health, the National Library of Medicine.

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