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ngs-dna-variant-calling

Routes WGS, WES, and panel DNA variant requests to germline, somatic, or UMI workflows.

5.3k|765|Updated Mar 4, 2026
Search Tags:#bioinformatics#nf-core#ngs#variant calling#wgs#WES#gatk4
One-click install
npx skills add https://github.com/openai/plugins --skill ngs-dna-variant-calling
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ngs-dna-variant-calling
Source: https://github.com/openai/plugins/tree/main/plugins/ngs-analysis/skills/ngs-dna-variant-calling
Command: npx skills add https://github.com/openai/plugins --skill ngs-dna-variant-calling

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

DNA variant calling requests vary widely by assay and sample model, and running one generic pipeline on germline, somatic, or UMI-panel data produces incorrect assumptions and unreliable calls. This Skill classifies the request and dispatches it to the correct subtype workflow before any execution.

Core Features & Use Cases

  • Request Classification: Routes WGS, WES, or targeted panel requests to germline, somatic, or UMI-panel subtype skills based on sample model and input type (FASTQ, BAM, CRAM).
  • Public Workflow Planning: Prefers nf-core/sarek for end-to-end runs, with GATK4, DeepVariant, samtools, and bcftools for focused tasks.
  • Local Execution Package: Runs a compact BAM/CRAM-to-VCF pipeline with region filtering, depth summaries, and resource readiness artifacts.
  • Use Case: A researcher with tumor-normal WES BAM files gets routed to the somatic subtype skill, then receives a preflight-checked nf-core/sarek plan with the correct target BED and pair metadata verified.

Quick Start

Classify my DNA sequencing run, choose germline, somatic, or UMI-panel routing, and prepare a preflight-first variant calling plan.

Frequently Asked Questions about ngs-dna-variant-calling

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

FAQPage Schema
How do I choose between germline and somatic variant calling?▼

Choose based on the sample model: germline covers inherited variants in single samples, cohorts, trios, and families, while somatic covers tumor-normal, tumor-only, or relapse-baseline cancer comparisons. This Skill routes the request once the sample model is confirmed.

What pipeline should I use for WGS or WES variant calling?▼

nf-core/sarek is the preferred public end-to-end workflow for WGS and WES data. Use direct GATK4, DeepVariant, samtools, or bcftools commands only for smaller focused tasks or when a custom pipeline is explicitly required.

Can I run variant calling directly from BAM or CRAM files?▼

Yes, the local runner accepts a sample sheet with BAM or CRAM columns plus a matching reference FASTA and produces a VCF. With a region specified it also emits per-base depth and callable-loci summaries, and optional quality filters produce a soft-filtered VCF.

How is UMI or duplex panel data handled differently?▼

UMI, duplex, and molecular-barcode panels are routed to a dedicated UMI-panel subtype skill that preserves barcode handling and molecule-level QC. Running a generic caller on low-frequency UMI data loses the error-correction assumptions these assays require.

What inputs are required before starting a variant calling run?▼

Confirm the data type (WGS, WES, or panel), sample model, input format, organism and reference genome, known-sites resources for BQSR, target BED for WES or panels, UMI handling, and desired callers and annotation outputs.

Why must genome builds match across reference files?▼

Mixing genome builds across FASTA, GTF/BED, known sites, and VEP cache produces misaligned coordinates and invalid variant calls. All reference resources must use the same build, such as GRCh38, before execution.

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