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bio-gatk-variant-calling
Maintainer FreedomIntelligence · Last updated April 1, 2026
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-gatk-variant-calling
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- GATK HaplotypeCaller is the gold standard for germline variant calling. This skill covers the GATK Best Practices workflow.
- gatk GenomicsDBImport \ --genomicsdb-workspace-path genomicsdb \ --sample-name-map sample_map.txt \ -L intervals.interval_list.
Source Doc
Excerpt From SKILL.md
Prerequisites
BAM files should be preprocessed:
- Mark duplicates
- Base quality score recalibration (BQSR) - optional but recommended
Single-Sample Calling
Goal: Call germline SNPs and indels from a single sample using HaplotypeCaller.
Approach: Run local de novo assembly of haplotypes in active regions to detect variants with optional annotation enrichment.
"Call variants from my BAM file using GATK" → Perform local haplotype assembly and genotyping on aligned reads using HaplotypeCaller.
GVCF Workflow (Recommended for Cohorts)
Goal: Enable joint genotyping across a cohort by generating per-sample genomic VCFs.
Approach: Call each sample in GVCF mode (-ERC GVCF), combine into a GenomicsDB or merged GVCF, then jointly genotype.
The GVCF workflow enables joint genotyping across samples for better variant calls.
Use cases
- Use when calling variants with GATK HaplotypeCaller.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- variant-calling - bcftools alternative
- alignment-files - BAM preprocessing
- filtering-best-practices - Post-calling filtering
- variant-normalization - Normalize before annotation
- vep-snpeff-annotation - Annotate final calls
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