skills.rest
stellaromics
stellaromicsOFFICIAL
Explore all skills by this author →
GitHub

bio-workflows-somatic-variant-pipeline

Call somatic mutations from tumor-normal paired samples using Mutect2 or Strelka2.

Updated Aug 23, 2026
Search Tags:#pipeline#annotation#cancer-genomics#somatic#variant-calling#mutect2#strelka2
One-click install
npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-workflows-somatic-variant-pipeline
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-workflows-somatic-variant-pipeline
Source: https://github.com/stellaromics/fast-bioinfo/tree/main/.claude/agents/spatial-analysis/skills/bio-workflows-somatic-variant-pipeline
Command: npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-workflows-somatic-variant-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Orchestrates end-to-end somatic variant discovery from tumor-normal paired samples, automating preprocessing, variant calling, filtering, and annotation to produce a final somatic VCF suitable for downstream analysis.

Core Features & Use Cases

  • End-to-end workflow covering preprocessing (duplication marking, base quality recalibration), somatic calling with Mutect2 or Strelka2, filtering to remove artifacts and contamination, and functional annotation (Funcotator/VEP).
  • Supports tumor-normal paired samples with optional tumor-only mode, panel of normals, and gnomad-based filtering for robust somatic discovery.
  • Produces annotated, ready-to-analyze VCFs and summary reports for cancer genomics research and translational studies.

Quick Start

Provide tumor-normal BAMs and a reference genome to run the pipeline and produce a filtered, annotated somatic VCF.

Frequently Asked Questions about bio-workflows-somatic-variant-pipeline

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

FAQPage Schema
How do I call somatic mutations from tumor-normal paired BAM files?▼

This somatic variant calling pipeline supports tumor-only mode by applying panel of normals (PON) and gnomad-based filtering to identify somatic mutations without a matched normal control sample.

What is the difference between Mutect2 and Strelka2 for cancer genomics variant calling?▼

Mutect2 and Strelka2 are both supported somatic callers within this cancer genomics pipeline, allowing you to choose either tool to discover somatic variants from tumor-normal paired samples.

Do I need a panel of normals to run somatic variant calling?▼

A panel of normals is not strictly required but is supported as an optional resource for PON-based filtering to remove common artifacts and improve somatic variant discovery accuracy.

How do I annotate somatic variants in a VCF file for cancer research?▼

To annotate somatic variants, the workflow integrates Funcotator or VEP to add functional annotations to the filtered VCF, producing an annotated, ready-to-analyze file for downstream cancer genomics research.

Does the somatic variant pipeline handle preprocessing steps like base quality recalibration?▼

Yes, the somatic variant pipeline automates preprocessing steps including duplication marking and base quality recalibration before proceeding to variant calling and filtering.

Related Skills

Explore More Education & Research Skills→
TianGzlabTianGzlab
155

genomics-cnv-calling

Detect copy number variants from exome or whole-genome sequencing data using CNVkit, GATK gCNV, or Control-FREEC.

Official
Advanced
jaechang-hitsjaechang-hits
298

cbioportal-database

Retrieve cancer genomics data from the cBioPortal REST API.

Community
Intermediate
TianGzlabTianGzlab
155

genomics-variant-calling

Call germline and somatic SNVs and Indels from SAM/BAM files to VCF.

Official
Advanced
felixboehmfelixboehm

cbioportal-database

Query cBioPortal REST API for cancer genomics data and survival correlations.

Community
Advanced