Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-somatic-variant-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Tumor-normal somatic variant calling with GATK Mutect2/Strelka2.

OpenClawNanoClawAnalysisReproductionbio-workflows-somatic-variant-pipeline🧠 bioos extended suitebioos extended bioinformatics suitetumor

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-somatic-variant-pipeline

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow for calling somatic mutations from tumor-normal paired samples.
for normal in normal1.bam normal2.bam normal3.bam; do sample=$(basename $normal.bam) gatk Mutect2 \ -R reference.fa \ -I $normal \ --max-mnp-distance 0 \ -O ${sample}.vcf.gz done.

Source Doc

Excerpt From SKILL.md

Combine into PON

gatk GenomicsDBImport
-R reference.fa
--genomicsdb-workspace-path pon_db
-V normal1.vcf.gz
-V normal2.vcf.gz
-V normal3.vcf.gz
-L intervals.bed

gatk CreateSomaticPanelOfNormals
-R reference.fa
-V gendb://pon_db
-O pon.vcf.gz


## Step 5: Filter Variants

```bash
gatk FilterMutectCalls \
    -R reference.fa \
    -V unfiltered.vcf.gz \
    --contamination-table contamination.table \
    --tumor-segmentation segments.table \
    --ob-priors read-orientation-model.tar.gz \
    -O filtered.vcf.gz

## Extract PASS variants

bcftools view -f PASS filtered.vcf.gz -Oz -o somatic_final.vcf.gz

Use cases

Use bio-workflows-somatic-variant-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-somatic-variant-pipeline to sequencing, variant, or omics analysis tasks.