ngs-dna-somatic-variants Skill
Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks. Published by openai in plugins.
What is ngs-dna-somatic-variants Skill?
Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks. Published by openai in plugins. This profile combines repository metadata with install, compatibility, and usage signals so developers can quickly decide whether it fits their agent workflow before opening the source repository.
Automated repository signals based on public metadata such as recency, license, installation evidence, and adoption. These are not a security audit or endorsement.
Key capabilities
- Includes SKILL.md support
- Reusable instructions support
- Data analysis
- Design and media
- Data analysis use cases
- Design and media use cases
Technical details
- Install or run with Copy skill directory
When to use ngs-dna-somatic-variants Skill
- Use it for data analysis.
- Use it for design and media.
Built with
Editorial notes
Source
- Creator: openai
- Repository: openai/plugins
- Skill file: plugins/ngs-analysis/skills/ngs-dna-somatic-variants/SKILL.md
What it does
Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.
Skill instructions
Somatic DNA Variants Use this skill for tumor-normal or tumor-only somatic SNV/indel calling from FASTQ, BAM, or CRAM. If the request is inherited germline calling or family analysis, use ngs-dna-germline-variants. Essential Inputs Confirm: - tumor-normal, tumor-only, relapse-baseline, or multi-tumor design - WGS, WES, or panel assay and target BED when applicable - input type and whether reads are already aligned - tumor/normal pairing table and sample identifiers - reference build, known-sites, germline resource, and annotation cache - panel-of-normals availability and matched-normal availability - tumor purity, contamination expectations, and minimum allele fraction goals - desired outputs: raw calls, filtered calls, VEP/SnpEff annotation, MAF, CNV/SV handoff Route Prefer nf-core/sarek for an end-to-end public workflow when its supported callers fit the request. Use direct GATK Mutect2 or bcftools/samtools utilities for focused validation or prepared BAMs. Preflight command: bash py
Explore related resources
Frequently asked questions
What is ngs-dna-somatic-variants?
ngs-dna-somatic-variants is a open-source AI agent skill with Copy skill directory. Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.
Who is ngs-dna-somatic-variants best for?
ngs-dna-somatic-variants is best for reusing agent instructions, scripts, and references, data analysis workflows, design and media workflows.
How do I install ngs-dna-somatic-variants?
Install or run ngs-dna-somatic-variants using Copy skill directory. Check ngs-dna-somatic-variants for the latest setup command.
Is ngs-dna-somatic-variants actively maintained?
ngs-dna-somatic-variants may need a closer maintenance check before production use.
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