# Gatk Haplotypecaller

> Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.

- Skill: `vimalinx/gatk-haplotypecaller` (Agent Skill)
- Install (CLI): `npx skillmds add vimalinx/gatk-haplotypecaller`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/gatk-haplotypecaller/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/gatk-haplotypecaller

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# gatk-haplotypecaller

## Quick Start
- **Command:** `gatk HaplotypeCaller`
- **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

- Per-sample germline SNP and indel calling from analysis-ready BAM or CRAM files.
- Emitting reference-confidence gVCFs for later joint genotyping.
- Standard Broad/GATK-style germline workflows after alignment, duplicate handling, and BQSR.

## Common Patterns

```bash
gatk HaplotypeCaller \
  -R reference.fa \
  -I sample.analysis_ready.bam \
  -O sample.g.vcf.gz \
  -ERC GVCF
```

## Guardrails

- Input BAM or CRAM should already be analysis-ready and matched to the exact reference build.
- Joint calling workflows usually want `-ERC GVCF`, not a raw single-sample VCF.
- This skill definition only proves the workflow step is known; the local `gatk` executable still has to exist for real execution.