
Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
License: GNU GPLv3+, due to use of the GNU Scientific Library
Version: 1.21 (using htslib 1.21)

Usage:   bcftools [--version|--version-only] [--help] <command> <argument>

Commands:

 -- Indexing
    index        index VCF/BCF files

 -- VCF/BCF manipulation
    annotate     annotate and edit VCF/BCF files
    concat       concatenate VCF/BCF files from the same set of samples
    convert      convert VCF/BCF files to different formats and back
    head         view VCF/BCF file headers
    isec         intersections of VCF/BCF files
    merge        merge VCF/BCF files files from non-overlapping sample sets
    norm         left-align and normalize indels
    plugin       user-defined plugins
    query        transform VCF/BCF into user-defined formats
    reheader     modify VCF/BCF header, change sample names
    sort         sort VCF/BCF file
    view         VCF/BCF conversion, view, subset and filter VCF/BCF files

 -- VCF/BCF analysis
    call         SNP/indel calling
    consensus    create consensus sequence by applying VCF variants
    cnv          HMM CNV calling
    csq          call variation consequences
    filter       filter VCF/BCF files using fixed thresholds
    gtcheck      check sample concordance, detect sample swaps and contamination
    mpileup      multi-way pileup producing genotype likelihoods
    polysomy     detect number of chromosomal copies
    roh          identify runs of autozygosity (HMM)
    stats        produce VCF/BCF stats

 -- Plugins (collection of programs for calling, file manipulation & analysis)
    39 plugins available, run "bcftools plugin -lv" to see a complete list

 Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
 automatically even when streaming from a pipe. Indexed VCF and BCF will work
 in all situations. Un-indexed VCF and BCF and streams will work in most but
 not all situations.

