vcf-isec

name	vcf-isec
description	Use when you need to compute intersections, unions, or complements between bgzipped and tabix-indexed VCF or tab-delimited files.
disable-model-invocation	true
user-invocable	true

vcf-isec

Quick Start

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

When To Use This Tool

• Compute intersections, unions, complements, or Venn-style set outputs across multiple indexed VCFs.
• Compare concordance or exclusivity between callsets.
• Work on either VCFs or other tab-delimited region files when positions are indexable.
• Use it when set logic matters more than multi-sample merging.

Common Patterns

# 1) Keep positions present in at least two files
vcf-isec \
  -n +2 \
  a.vcf.gz b.vcf.gz c.vcf.gz \
  > shared.vcf

# 2) Output positions unique to the first file
vcf-isec \
  -c \
  a.vcf.gz b.vcf.gz c.vcf.gz \
  > a_only.vcf

# 3) Create Venn-style output files
vcf-isec \
  -p isec_out \
  a.vcf.gz b.vcf.gz c.vcf.gz

Recommended Workflow

1. Bgzip and index all inputs first.
2. Decide whether you want count-based set logic (-n), complement (-c), or multi-output decomposition (-p).
3. Add -a if you want to ignore non-PASS records during comparison.
4. Review outputs carefully because records from different files can intermix in surprising ways.

Guardrails

• Inputs must be bgzipped and tabix-indexed unless you are using the tab-delimited mode explicitly with -t.
• -f forces past differing columns or VCF versions; only do that when you understand the compatibility risk.
• -o prints only entries from the left-most file even when set logic uses all files.
• Nearby indels may be normalized differently across callers, so -w can materially change what is considered shared.