gatk-haplotypecaller

name	gatk-haplotypecaller
description	Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
disable-model-invocation	true
user-invocable	true

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.