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Bcftools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Bcftools is designed to work on a stream. It regards an input file "-" as the standard input (stdin) and an output file "-" as the standard output (stdout). Several commands can thus be combined with Unix pipes.

Please feel free to expand and improve these pages.

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List of commands

• tabix .. tabix for BGZF'd BED, GFF, SAM, VCF and more
• index .. index BCF

Core VCF/BCF tools:

• annotate .. annotate and edit VCF/BCF files
• call .. SNP/indel calling (former "view")
• filter .. filter VCF/BCF files using fixed thresholds
• isec .. intersections of VCF/BCF files
• merge .. merge VCF/BCF files
• norm .. normalize indels
• query .. transform VCF/BCF into user-defined formats
• stats .. produce VCF/BCF stats (former vcfcheck)
• subset .. subset and filter VCF/BCF files
• view .. VCF<->BCF conversion

Other/Experimental tools:

• gtcheck .. check sample concordance, detect swaps and contaminations