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Gatk Haplotypecaller

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

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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

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.

vimalinx/bio-agent/tree/main/.claude/skills/gatk-haplotypecaller commit 851428486e

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npx skillmds add vimalinx/gatk-haplotypecaller