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Open sourceGenomics & SequencingLibraries & SDKs

BCFtools

Call, filter and manipulate genomic variants (VCF/BCF)

WebsiteSource codeDocumentationPublication

BCFtools is the companion to SAMtools for variant data. It calls, filters, normalises, merges and annotates variants in VCF/BCF format.

Common commands

1bcftools mpileup -f ref.fa sample.bam | bcftools call -mv -Oz -o calls.vcf.gz
2bcftools view -i 'QUAL>30 && INFO/DP>10' calls.vcf.gz
3bcftools norm -f ref.fa -m- calls.vcf.gz -Oz -o norm.vcf.gz

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