VCFtools protocols

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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: 5758599
PMID: 29354142
DOI: 10.3389/fpls.2017.02185

[…] psti-ecot22i based on the max barcode size. the minmaf for the discoverysnpcallerpluginv2 was set to 0.01. all other default parameters were used. non-biallelic sites and indels were removed using vcftools v.0.1.14 (danecek et al., ). variant call format (vcf) files for both enzymes were then merged using a custom perl script, preferentially keeping snps called by psti-ecot22i at overlapping […]

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

[…] et al., ) by bwa (li and durbin, ). then snp/indel variants were called using gatk (mckenna et al., ; depristo et al., ). finally, snp/indel density was calculated from the variation data by vcftools (danecek et al., )., 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 [] 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 values […]

PMCID: 5795354
PMID: 29346588
DOI: 10.1093/gbe/evy007

[…] the californian samples. the first snps were a previously generated set of snps identified in native range african and european bees () and was used for all ancestry analyses. we used samtools/vcftools to generate snp calls for each individual, requiring a quality score of 30 for reads to be included. a minimum coverage of 7× was required to make genotype calls for an individual […]

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

[…] (eas)., to find the populations wise genetic differentiation with respect to cardiovascular diseases, pair-wise weir and cockerham fst [] 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 […]

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VCFtools in publications

PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] ()., we used filtered variants (vcf) to visualize relationships between isolates using principal-component analysis (pca) implemented in snprelate v.1.10.2 (). summary statistics were computed using vcftools (). neutrality tests were performed using angsd (). genetic clustering was performed using ngsadmix () and faststructure ()., the linkage disequilibrium was calculated as r2, which indicates […]

PMCID: 5931971
PMID: 29720620
DOI: 10.1038/s41467-018-04104-z

[…] in the supplementary information of a previous paper. the resulting vcf files were then combined with the vcf files downloaded from the pf3k project and filtered to remove non-variant sites using vcftools., to determine whether any previously implicated drug resistance snps were associated with ppqr, we analyzed the snps in the genes listed in the supplementary data . samples were divided […]

PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] to build the database for snpeff., to analyze the effects of single snps, the vcf files containing the lists of annotated snps for each sample were merged using the following command available from vcftools:, vcf-merge sample1.vcf.gz [...] samplex.vcf.gz | \, bgzip –c > merged.all.emit.confident.sites.vcf.gz, variant annotations of upstream and downstream snps located further than 100 bases […]

PMCID: 5960308
PMID: 29712833
DOI: 10.1073/pnas.1721749115

[…] with a step of 250 kb along all chromosomes, using the 19,615,087 high-quality snvs randomly distributed on chromosomes. genomic regions under selective sweeps were measured by the fst using vcftools v0.1.13 () with parameters of “–fst-window-size 1000000–fst-window-step 250000.” genomic regions with fst values >0.3 were considered under strong selective sweeps. genetic diversity (π) […]

PMCID: 5921299
PMID: 29703145
DOI: 10.1186/s12864-018-4673-2

[…] version 1.6 []. the resulting sequences where aligned using clustal omega [], the alignment was checked and trimmed in phyde version 0.9971 []. calculations were done using dnasp version 6.10.03 [], vcftools version 0.1.15 [] and microsoft excel 2016., additional file 1: additional file 2: additional file 3: additional file 4: additional file 5: additional file 6: additional file 7: additional […]

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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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