Vcf Isec

# 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.