BCFtools

Overview

BCFtools is a high-performance toolkit for manipulating variant calls stored in VCF and BCF format. It provides sub-commands for filtering, merging, splitting, subsetting, normalising, and computing statistics on variant files. BCFtools uses streaming and indexing strategies that allow it to process large whole-genome VCFs efficiently with low memory usage. It is the variant-file counterpart to SAMtools and shares the same HTSlib backend for reading and writing compressed, indexed genomic data files.

Installation

mamba install -c bioconda bcftools

Basic Usage

Quality filtering

Apply minimum quality and depth filters to a VCF file.

bcftools filter -i 'QUAL>=20 && INFO/DP>=10' \
  clair3_output/merge_output.vcf.gz \
  -Oz -o filtered.vcf.gz

Separate SNPs and indels

bcftools view -v snps filtered.vcf.gz -Oz -o snps.vcf.gz
bcftools view -v indels filtered.vcf.gz -Oz -o indels.vcf.gz

Generate statistics

bcftools stats filtered.vcf.gz > variant_stats.txt
bcftools stats snps.vcf.gz > snp_stats.txt

Key Parameters

Flag / option	Description
`filter -i EXPR`	Include only records matching the expression (e.g. `'QUAL>=20 && INFO/DP>=10'`).
`filter -e EXPR`	Exclude records matching the expression.
`view -v TYPE`	Select variant types: `snps`, `indels`, `mnps`, or `other`.
`view -s SAMPLE`	Subset the VCF to specific samples.
`view -r REGION`	Restrict output to a genomic region (e.g. `chr1:1000-2000`).
`-Oz`	Write output as bgzip-compressed VCF.
`-Ob`	Write output as BCF (binary VCF).
`-o FILE`	Output file path.
`stats`	Compute per-sample and per-site variant statistics.
`merge`	Merge multiple VCF/BCF files from non-overlapping sample sets.
`norm`	Left-align and normalise indels; split multi-allelic sites.
`query -f FORMAT`	Extract specific fields in a custom output format.

Expected Output

filtered.vcf.gz – a compressed VCF containing only variants that pass the specified filter criteria.
snps.vcf.gz / indels.vcf.gz – VCF files separated by variant type.
variant_stats.txt – a comprehensive text report including counts of SNPs, indels, MNPs, transitions/transversions ratio (Ts/Tv), per-sample statistics, indel length distributions, and quality score distributions. This file can be visualised with plot-vcfstats:

plot-vcfstats variant_stats.txt -p stats_plots/