AI Plugin Index
ngs-dna-germline-variants
Skill by openai · updated · ★ 7.6k
Runs or plans germline DNA variant calling for WGS, WES, and targeted panel data, from FASTQ, BAM, or CRAM. It is for analysts working on singleton, cohort, duo, or trio samples. ngs-dna-germline-variants is published by openai on GitHub.
Install ngs-dna-germline-variants
Built from the published package, never by AIgit clone --depth 1 https://github.com/openai/plugins /tmp/plugins && mkdir -p ~/.claude/skills && cp -r /tmp/plugins/plugins/ngs-analysis/skills/ngs-dna-germline-variants ~/.claude/skills/ngs-dna-germline-variantsRun in your terminal. Claude Code loads skills from ~/.claude/skills automatically.
Step-by-step: install ngs-dna-germline-variants in Claude Code
git clone --depth 1 https://github.com/openai/plugins /tmp/plugins && mkdir -p ~/.gemini/antigravity-cli/skills && cp -r /tmp/plugins/plugins/ngs-analysis/skills/ngs-dna-germline-variants ~/.gemini/antigravity-cli/skills/ngs-dna-germline-variantsAntigravity CLI loads skills from ~/.gemini/antigravity-cli/skills, or .agents/skills for one project.
Step-by-step: install ngs-dna-germline-variants in Antigravity CLI
Skills can run scripts on your machine. Some need an API key: check the README.
Last commit 16 days ago
No licence found, so reuse rights are unclear
Clear description, installs from GitHub, 7,567 stars, original repository
No risky patterns in the files we checked
About ngs-dna-germline-variants
This skill guides germline variant calling workflows for WGS, WES, and inherited-disease panel data. It covers singleton, cohort, duo, trio, family, and case/control sample models. It checks reference build, known-sites resources, target BED files, and sex or ploidy assumptions before a run.
The skill prefers nf-core/sarek for full FASTQ or BAM-to-VCF workflows and uses GATK4, DeepVariant, samtools, or bcftools for focused tasks. It includes script-based runners for local samtools/bcftools runs and for GATK-based runs with BQSR, per-sample gVCFs, and joint genotyping. Outputs include a QC summary, VCF or gVCF paths, and annotation paths. It is aimed at bioinformatics teams doing germline analysis.
Written from the project's SKILL.md and checked against it.
What ngs-dna-germline-variants can do
- Workflow routingChooses between nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools based on the task.
- Input checksConfirms data type, sample model, input format, reference build, and known-sites resources before running.
- Preflight planRuns a preflight check that can emit an install plan for the DNA germline pipeline.
- Focused variant callingRuns a compact samtools/bcftools calling pass from prepared BAM or CRAM files.
- Germline runnerRuns a local GATK-based workflow with BQSR, per-sample gVCFs, and optional joint calling.
- QC summaryReports coverage, duplication, insert size, contamination, and sex or relatedness checks when run.
- Resource manifestWrites resource plan, manifest, environment, and readiness files for reference and known-sites bundles.
- Trio and family handlingKeeps pedigree metadata and reports Mendelian and QC checks separately from interpretation.
What you need
- Python
- Prepared FASTQ, BAM, or CRAM files
- Reference FASTA with matching indexes
- Reference-matched known-sites resources
- GATK toolchain for the germline runner
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Try asking
- Plan a germline WES variant calling workflow for a family trio
- Check my reference build and known-sites files before BQSR
- Run the germline runner on my cohort with gVCFs and joint calling
Good to know
- Not for tumor-only, tumor-normal, or UMI-based somatic panel calling.
- Clinical interpretation, pathogenicity classification, and report signing are out of scope.
- BQSR requires reference-matched known-sites resources; mixed builds should not be used.
- The germline runner packages validation state even when execution is blocked by missing tools or resources.
Security check
ANo download-and-run commands, hidden instructions or signs of sending keys out were found.
Checked automatically: plugins/ngs-analysis/skills/ngs-dna-germline-variants/SKILL.md. This looks for known risky patterns and is not a full audit. How grades work
Inside the skill
-
SKILL.md4 KB -
agents/openai.yaml300 B
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ngs-dna-germline-variants: common questions
Does this skill interpret variants clinically?
No. The source says clinical interpretation, pathogenicity classification, and report signing are out of scope unless the user provides a validated clinical workflow.
Which sequencing data types does it support?
The source names WGS, WES, and targeted panel data, from FASTQ, BAM, or CRAM input.
When should I use this instead of a somatic skill?
Use this skill for germline WGS, WES, or inherited-disease panels. The source says tumor-only, tumor-normal, and low-frequency UMI panel calling need a somatic or UMI-panel skill.
How do I install ngs-dna-germline-variants?
Run the command above to copy the skill into ~/.claude/skills/. Claude Code picks it up automatically.
Is ngs-dna-germline-variants free?
The code is public, but no licence file was found, so check the repository before commercial use.
Is ngs-dna-germline-variants safe to use?
It scores 85 of 100. Grades: maintenance A, licence F, quality A. Security check: grade A, no risky patterns found in the files checked. Review the code before you install. How grades work.
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