Vcftools
- fill-aa(1) fill in ancestral alleles
- fill-an-ac(1) fill or recalculate AN and AC INFO fields.
- fill-fs(1) Annotate VCF with flanking sequence
- fill-ref-md5(1) computes MD5 sum of the reference sequence
- fill-rsIDs(1) fill missing rsIDs
- vcf-annotate(1) annotate VCF file, add filters or custom annotations
- vcf-compare(1) compare bgzipped and tabix indexed VCF files
- vcf-concat(1) concatenate VCF files
- vcf-consensus(1) vcf-consensus
- vcf-contrast(1) finds differences amongst samples
- vcf-convert(1) convert between VCF versions
- vcf-fix-newlines(1) fix newlines in VCF file
- vcf-fix-ploidy(1) vcf-fix-ploidy
- vcf-indel-stats(1) vcf-indel-stat
- vcf-isec(1) create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
- vcf-merge(1) merge the bgzipped and tabix indexed VCF files
- vcf-phased-join(1) take multiple overlapping pre-phased chunks and concatenates them into one VCF
- vcf-query(1) query VCF files
- vcf-shuffle-cols(1) reorder columns
- vcf-sort(1) sort VCF file
- vcf-stats(1) statistic of VCF file
- vcf-subset(1) create subset of VCF file
- vcf-to-tab(1) convert to tabix
- vcf-tstv(1) vcf-tstv
- vcf-validator(1) validate VCF file
- vcftools(1) Utilities for the variant call format (VCF) and binary variant call format (BCF)