Man Pages in vcftools

Section 1: Executable programs or shell commands

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-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

Analyse vcf files