| 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.
