# Vcf Validator

> Use when you need to validate VCF files for format compliance and detect issues like duplicate positions.

- Skill: `vimalinx/vcf-validator` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add vimalinx/vcf-validator`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/vcf-validator/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/vcf-validator

---


# 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

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

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

```bash
# 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.