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

VCFtools article

VCFtools citations

PMCID: 5805289

[…] 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: 5767965

[…] et al. 2010). to investigate the effect of inbreeding on this population’s parameters, 82 of the most inbred lines were reanalyzed (data not shown). the coefficient of inbreeding was calculated using vcftools (v0.1.14) (danecek et al. 2011). the quality of variant calls was also compared with the level of heterozygosity for all lines. we examined the effect of masking heterozygous bases and exclud […]

PMCID: 5711884

[…] of test statistics. eigenvectors for the gwas data sets were inferred using smartpca (part of eigensoft) by merging cases and controls with phase iii hapmap samples. ld metrics were calculated in vcftools v0.1.12b67, using uk10k merged 1000 genomes project data and plotted using vispig68., the eight snps in the most promising loci (table 1; supplementary table 6 ), were taken forward for de […]

PMCID: 5667528

[…] 238,493,056), the pipeline found 476,589 tags, aligned with bowtie2 software. the tag mapping and the polymorphism calling identified 109,201 polymorphic sites. the data were further processed with vcftools [34]. indels and snps that were not biallelic were discarded. data points with a sequencing depth of less than five were set to missing. snps with more than 50% missing data were discarded. […]

PMCID: 5552344

[…] increasing physical distance between snps due to meiotic recombination. the squared correlation coefficient r2 between pairs of snps of varying distance across the same chromosome was measured using vcftools; r2 values were binned by distance (50-bp windows) and medians within each window were plotted against physical distance between snps. the level of background ld between unlinked markers […]

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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