BCFtools.md

Update: 2025.6.2 Reference: BCFtools GitHub

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1. BCFtools view

The bcftools view command is used for converting and filtering BCF/VCF files.

Examples:

# View the content of a compressed BCF file and convert it to compressed VCF format
bcftools view -Oz -o output.vcf.gz input.bcf

# Use the `-O` option to specify output format:
# - `b`: Compressed BCF
# - `u`: Uncompressed BCF
# - `z`: Compressed VCF
# - `v`: Uncompressed VCF

# Filter by region, retaining only chr1 positions between 1,000,000 and 2,000,000
bcftools view -r chr1:1000000-2000000 -Oz -o region_filtered.vcf.gz input.bcf

# Filter using multiple regions specified in a file (in BED format)
bcftools view -R regions.bed -Oz -o file_filtered.vcf.gz input.bcf

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2. BCFtools call

The bcftools call command is used for variant calling.

Examples:

# Perform variant calling using the `-m` algorithm for multi-allelic variant detection
bcftools mpileup -Ou -f reference.fa input.bam | bcftools call -mv -Oz -o output_variants.vcf.gz

# View the content of a compressed VCF file without decompression
zcat output_variants.vcf.gz | head -n 20

# Filter all variant lines (excluding headers) using `grep`
zcat output_variants.vcf.gz | grep -v "^#"

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This cheatsheet provides concise usage examples for common BCFtools commands, making it an essential reference for bioinformatics workflows. For detailed documentation, visit the official BCFtools documentation.