# Gatk Genotypegvcfs

> Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.

- Skill: `vimalinx/gatk-genotypegvcfs` (Agent Skill)
- Install (CLI): `npx skillmds@latest add vimalinx/gatk-genotypegvcfs`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/gatk-genotypegvcfs/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Data & Analytics
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/gatk-genotypegvcfs

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# gatk-genotypegvcfs

## Quick Start
- **Command:** `gatk GenotypeGVCFs`
- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/gatk`
- **Install hint:** Install GATK into the active bioinformatics environment or put a working `gatk` executable on `PATH`.

## When To Use This Tool

- Joint-genotyping per-sample gVCFs into a cohort VCF.
- Standard downstream step after producing reference-confidence gVCFs with HaplotypeCaller.
- Germline SNP/indel discovery workflows for WES or WGS cohorts.

## Common Patterns

```bash
gatk GenotypeGVCFs \
  -R reference.fa \
  -V cohort.g.vcf.gz \
  -O cohort.joint.vcf.gz
```

## Guardrails

- Input gVCFs must have been generated against the same reference build and compatible interval scheme.
- This skill definition only proves the workflow step is known; the local `gatk` executable still has to exist for real execution.