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ngs-dna-somatic-variants

Plan and run tumor-normal or tumor-only somatic SNV/indel calling workflows from FASTQ, BAM, or CRAM.

5.3k|765|Updated Mar 4, 2026
Search Tags:#bioinformatics#somatic variants#ngs#variant calling#wgs#mutect2#tumor-normal
One-click install
npx skills add https://github.com/openai/plugins --skill ngs-dna-somatic-variants
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ngs-dna-somatic-variants
Source: https://github.com/openai/plugins/tree/main/plugins/ngs-analysis/skills/ngs-dna-somatic-variants
Command: npx skills add https://github.com/openai/plugins --skill ngs-dna-somatic-variants

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Somatic variant calling requires careful tumor-normal pairing, contamination checks, panel-of-normals selection, and purity-aware filtering; mistakes in any of these steps silently corrupt results. This Skill structures the entire workflow so pairing, resources, and QC are verified before and after execution.

Core Features & Use Cases

  • Workflow Planning and Routing: Confirms design (tumor-normal, tumor-only, relapse-baseline, multi-tumor), assay type (WGS, WES, panel), and routes to nf-core/sarek or a direct GATK Mutect2 runner.
  • Resource and Pairing Validation: Generates pairing tables, resource manifests, readiness reports, and advisory checks for reference builds, germline resources, and panels of normals.
  • QC and Review Outputs: Produces contamination/filtering artifacts, somatic QC summaries, per-pair review tables, and filtered VCF outputs.
  • Use Case: Given a tumor-normal WES cohort with prepared BAMs, run the preflight check, verify the pairing table and PON compatibility, then execute Mutect2 and review the filtered call counts and QC summary.

Quick Start

Plan a tumor-normal somatic variant-calling workflow from my BAM files, verify the pairing and reference resources, and run the preflight check before executing Mutect2.

Frequently Asked Questions about ngs-dna-somatic-variants

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run tumor-normal somatic variant calling with Mutect2?▼

Somatic variant calling with Mutect2 requires a validated tumor-normal pairing table, a reference FASTA, a germline resource, and optionally a panel of normals. The runner script generates the pairing table, command plan, contamination artifacts, and filtered VCF outputs when local GATK resources are available.

What is the difference between nf-core/sarek and direct Mutect2 for somatic calling?▼

nf-core/sarek provides an end-to-end public workflow from raw reads through calling, while the direct Mutect2 runner targets focused validation on already-prepared tumor/normal BAM or CRAM files. Choose sarek for full pipelines and the direct runner for compact local checks.

Can I do somatic variant calling without a matched normal sample?▼

Tumor-only calling is supported but carries elevated false-positive risk and requires a germline resource plus careful filtering. Results should not be presented as confirmed somatic without supporting evidence, and a panel of normals is strongly recommended.

Can I reuse a panel of normals across different capture kits?▼

No, a panel of normals must be reference-matched and compatible with the capture kit and genome build used for the tumor samples. Reusing a PON across incompatible kits or builds introduces systematic artifacts into the filtered calls.

What QC metrics should I check for somatic variant workflows?▼

Track contamination, orientation bias, strand artifacts, mapping quality, coverage depth, duplication, insert size, tumor purity, and allele-fraction filters. For WES and panel assays, also verify on-target rate before interpreting filtered call counts.

Does this workflow provide clinical treatment recommendations?▼

No, clinical actionability and treatment recommendations are out of scope. The workflow produces filtered VCF/MAF outputs and QC summaries, and clinical interpretation requires a separately validated clinical workflow supplied by the user.

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