vcf-validator

name	vcf-validator
description	Use when you need to validate VCF files for format compliance and detect issues like duplicate positions.
disable-model-invocation	true
user-invocable	true

vcf-validator

Quick Start

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

When To Use This Tool

• Check whether a VCF is structurally valid before indexing, merging, or handing it to stricter downstream software.
• Detect duplicate positions that may break assumptions in later tools.
• Collapse repeated warning types to a single message when triaging noisy files.

Common Patterns

# 1) Basic validation
vcf-validator file.vcf.gz

# 2) Warn about duplicate positions too
vcf-validator -d file.vcf.gz

# 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.