bio-workflows-somatic-variant-pipeline

npx skills add BioTender-max/awesome-bio-agent-skills --skill somatic-variant-pipeline --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: CNVkit 0.9+, Ensembl VEP 111+, GATK 4.5+, SnpEff 5.2+, bcftools 1.19+, picard 3.1+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Somatic Variant Pipeline **"Call somatic mutations from my tumor-normal pair"** → Orchestrate alignment, Mutect2 somatic calling, contamination filtering, variant annotation (Funcotator/VEP), TMB calculation, and mutational signature analysis. Complete workflow for calling somatic mutations from tumor-normal paired samples. ## Pipeline Overview ``` Tumor BAM + Normal BAM │ ├── Preprocessing (if needed) │ └── MarkDuplicates, BQSR │ ├── Variant Calling │ ├── Mutect2 (GATK) - SNVs + indels │ └── Strelka2 - SNVs + indels (faster) │ ├── Filtering │ ├── FilterMutectCalls │ ├── Contamination estimation │ └── Orientation bias filtering │ ├── Annotation │ ├── Funcotator / VEP │ └── Cancer-specific databases │ └── Output: Filtered somatic VCF ``` ## Mute

Create PON from multiple normal samples
for normal in normal1.bam normal2.bam normal3.bam; do
gatk Mutect2 \
done
Combine into PON
gatk GenomicsDBImport \
gatk CreateSomaticPanelOfNormals \
gatk LearnReadOrientationModel \
gatk GetPileupSummaries \
gatk CalculateContamination \