bcftools

View a VCF/BCF file

$ bcftools view [input.vcf.gz]

$ bcftools view -r [chr1:1000000-2000000] [input.vcf.gz]

$ bcftools view -Ob -o [output.bcf] [input.vcf.gz]

$ bcftools mpileup -f [reference.fa] [aligned.bam] | bcftools call -mv -Oz -o [calls.vcf.gz]

$ bcftools merge [file1.vcf.gz] [file2.vcf.gz] -Oz -o [merged.vcf.gz]

$ bcftools filter -i 'QUAL>30 && DP>10' [input.vcf.gz] -Oz -o [filtered.vcf.gz]

$ bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' [input.vcf.gz]

$ bcftools index [input.vcf.gz]

bcftools subcommand [options] [file]

bcftools is a suite of utilities for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. It is part of the SAMtools/HTSlib project and is widely used in bioinformatics for genomic variant analysis.
All commands work transparently with both VCF and BCF files, compressed or uncompressed. The tools are designed to work in pipelines, reading from stdin and writing to stdout.

-Ob

Output compressed BCF

Output compressed VCF (bgzipped)

Output uncompressed VCF

Output uncompressed BCF (fastest for piping)

Restrict to regions (chr:from-to format)

Comma-separated list of samples to include

Include sites matching filter expression

Exclude sites matching filter expression

Output file name

Variant Calling

mpileup, call

view, merge, concat, sort, index, convert

filter, query, norm

stats, roh, gtcheck

annotate, csq, fill-tags

reheader, isec, +split, +scatter

consensus

Use -Ou when piping between bcftools subcommands to avoid unnecessary compression overhead. Indexed files are required for random access and some operations. VCF/BCF files should be sorted by chromosome and position for most operations.

bcftools was developed as part of the SAMtools project, initially created by Heng Li at the Wellcome Sanger Institute. It became a separate project around 2014 with the HTSlib library rewrite, gaining significant functionality for variant analysis.

samtools(1), tabix(1), bgzip(1)