bcftools

name	bcftools
description	Use when working with VCF/BCF variant files for indexing, manipulation, analysis, or variant calling.
disable-model-invocation	true
user-invocable	true

bcftools

Quick Start

• Command: bcftools
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bcftools
• Version: 1.22
• Full reference: See references/help.md for complete help text and subcommand details

When To Use This Tool

• Inspect, filter, normalize, query, call, and summarize VCF/BCF files.
• Default companion tool for modern variant workflows.
• Use it after alignment/variant calling and before downstream annotation or cohort comparison.
• Prefer subcommand-oriented use such as view, norm, query, stats, call, or mpileup.

Common Patterns

# 1) Subset and view a compressed VCF
bcftools view -r chr1:100000-110000 cohort.vcf.gz

# 2) Normalize variants against a reference
bcftools norm -f reference.fa -Oz -o cohort.norm.vcf.gz cohort.vcf.gz
bcftools index cohort.norm.vcf.gz

# 3) Extract tabular fields
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' cohort.vcf.gz

# 4) Produce summary statistics
bcftools stats cohort.vcf.gz > cohort.stats.txt

Recommended Workflow

1. Keep VCF/BCF indexed whenever possible.
2. Use view or filter to subset before heavier operations.
3. Normalize indels with norm before comparing or merging callsets.
4. Use query and stats for reporting instead of ad hoc parsing when possible.

Guardrails

• Indexed VCF/BCF works in all situations; streams and unindexed files do not.
• bcftools norm needs the correct reference FASTA to do honest left-alignment and normalization.
• Use plugin -lv before reinventing functionality that already exists in a plugin.
• Be explicit about compressed output with -Oz or BCF output with -Ob when building pipelines.