Command-line tool

bcftools

brew/bcftools

Checked 25 Oct 2026, 21:09 UTC · Listing refreshed from Homebrew, winget, npm, Scoop and cargo; npm packages checked against OSV.dev

Tools for BCF/VCF files and variant calling from samtools

Website

At a glance

Type

Command-line tool

Install on

macOS, Linux

Last checked

25 Oct 2026, 21:09 UTC

Install it

macOS

brew install bcftools

Linux

brew install bcftools

View BCF file and convert to [v]CF on `stdout`

bcftools view path/to/input.bcf -O v

Sort a VCF file variants by chromosome and position, output to a [b]CF file, and index the sorted output

bcftools sort path/to/input.vcf.gz -O b -o path/to/sorted.bcf -W

Concatenate sorted VCF files that share the same samples to [z]ipped VCF on `stdout`

bcftools concat path/to/chr1.vcf.gz path/to/chr2.vcf.gz ... -O z

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• slashem
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• byacc
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• echtvar
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