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gatk-variant-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

gatk-variant-calling.

OpenClawNanoClawAnalysisReproductiongatk-variant-callingopenclaw medical skillsadditional scientific toolsgatk

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gatk-variant-calling

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

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:

  1. Mark duplicates
  2. Base quality score recalibration (BQSR) - optional but recommended

GVCF Workflow (Recommended for Cohorts)

The GVCF workflow enables joint genotyping across samples for better variant calls.

From GenomicsDB

gatk GenotypeGVCFs
-R reference.fa
-V gendb://genomicsdb
-O cohort.vcf.gz

Use cases

  • Use gatk-variant-calling for genomics and bioinformatics workflows.
  • Apply gatk-variant-calling to sequencing, variant, or omics analysis tasks.

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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