vcf-compare

name	vcf-compare
description	Use when comparing two or more bgzipped and tabix-indexed VCF files to assess concordance of variant calls, positions, or genotypes.
disable-model-invocation	true
user-invocable	true

vcf-compare

Quick Start

• Command: vcf-compare [OPTIONS] file1.vcf.gz file2.vcf.gz ...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-compare
• Full reference: See references/help.md

When To Use This Tool

• Measure concordance between two or more indexed VCF callsets.
• Compare either positions only or full genotypes with -g.
• Generate per-chromosome comparison outputs and plotting summaries.
• Inspect indel comparison behavior with a tolerance window when callers left-align differently.

Common Patterns

# 1) Compare positions only
vcf-compare truth.vcf.gz calls.vcf.gz

# 2) Compare genotypes for matched samples
vcf-compare -g truth.vcf.gz calls.vcf.gz

# 3) Restrict to PASS records and make plots
vcf-compare \
  -a \
  -g \
  -p cmp_plots \
  truth.vcf.gz calls.vcf.gz

Recommended Workflow

1. Make sure all inputs are bgzipped and tabix-indexed before comparing.
2. Decide whether you care about positional concordance only or true genotype agreement with -g.
3. Use sample-name mapping if the files carry equivalent samples under different column names.
4. Review summary metrics and, for difficult cases, restrict to regions or apply a comparison window for indels.

Guardrails

• Inputs must be bgzipped and tabix-indexed.
• Without -g, this is mostly a position-level comparison, not a sample-genotype concordance audit.
• --ignore-indels and -w can materially change the biological interpretation of agreement.
• -c/--chromosomes is retained only for backward compatibility; prefer -r/--regions.