Vcf Validator

# 3) Show each message type only once
vcf-validator -u file.vcf.gz

Recommended Workflow

1. Validate the VCF before compression/index regeneration, merging, or cohort comparison.
2. Re-run with -d if positional duplication is a concern in your workflow.
3. Use -u for noisy failure cases so you can see the distinct categories of problems quickly.
4. Fix the source VCF rather than normalizing around repeated validator failures downstream.

Guardrails

• Use this as a structural sanity check, not as proof that the biological content is correct.
• Input is expected to be a VCF path in the style documented by the tool; compressed VCF is the common case in this workspace.
• --version is not supported in the usual way; use -h for interface help.
• Validation output can be noisy on badly malformed files, so -u is useful for triage but should not replace a full review.