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ngs-dna-germline-variants

Plan and run germline WGS, WES, and panel variant-calling workflows from FASTQ, BAM, or CRAM.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Setting up germline DNA variant-calling workflows requires coordinating reference builds, known-sites resources, sample models, QC checks, and caller selection, and mistakes in any of these produce invalid VCF results.

Core Features & Use Cases

  • Workflow Routing: Directs full FASTQ/BAM-to-VCF runs to nf-core/sarek and focused tasks to GATK4, DeepVariant, samtools, or bcftools.
  • Preflight Validation: Checks reference build, known-sites for BQSR, target BEDs, sample model, and resource readiness before execution.
  • Cohort and Trio Support: Handles singleton, cohort, duo, trio, and family models with gVCF emission, joint genotyping, and Mendelian QC checks.
  • Use Case: Given a trio WES dataset in CRAM format, generate a validated sarek or GATK4 command plan with BQSR known-sites, target BED handling, and a QC summary covering coverage, contamination, and sex concordance.

Quick Start

Ask the assistant to plan a germline variant-calling workflow for your WGS or WES samples, specifying the input format, reference build, and sample model.

Frequently Asked Questions about ngs-dna-germline-variants

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

FAQPage Schema
How do I run a germline variant-calling workflow on WGS data?▼

Use nf-core/sarek for full FASTQ/BAM-to-VCF workflows, or the provided germline runner script with a sample sheet, reference FASTA, and known-sites VCFs. Enable --emit-gvcf and --joint-call for cohort joint genotyping.

GATK4 vs DeepVariant for germline variant calling?▼

GATK4 supports BQSR, per-sample gVCFs, and joint genotyping for cohorts and trios. DeepVariant suits focused per-sample calling tasks. The skill routes full workflows to nf-core/sarek and focused tasks to direct callers.

Can I use BQSR without known-sites databases?▼

No. BQSR requires reference-matched known-sites resources such as dbSNP and Mills indels. Never mix GRCh37, hg19, GRCh38, or T2T resources, and skip BQSR when matched known-sites are unavailable.

Does this workflow support tumor-normal somatic calling?▼

No. Tumor-only, tumor-normal, and low-frequency UMI panel calling are out of scope and should use a somatic or UMI-panel skill instead. This workflow covers germline WGS, WES, and inherited-disease panels only.

What QC checks should I run on germline variant calls?▼

Check coverage, duplication rate, insert size, contamination, sample identity, sex concordance, and transition/transversion ratio where feasible. For trios, report Mendelian consistency checks separately from variant interpretation.

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