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vcftools

Tools for working with VCF (Variant Call Format) files

brewmacoslinux

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About

Tools for working with VCF files

Commands

vcftoolsvcf-concatvcf-mergevcf-sortvcf-subsetvcf-stats

Examples

Filter VCF file to keep only biallelic SNPs with minimum depth of 10$ vcftools --vcf input.vcf --remove-indels --min-meanDP 10 --recode --out filtered

Calculate basic VCF statistics$ vcftools --vcf input.vcf --freq --out stats

Extract specific samples from a VCF file$ vcftools --vcf input.vcf --keep samples.txt --recode --out subset