ngs-dna-germline-variants Skill
Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks. Published by openai in plugins.
What is ngs-dna-germline-variants Skill?
Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, 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
- Data analysis use cases
Technical details
- Install or run with Copy skill directory
When to use ngs-dna-germline-variants Skill
- Use it for data analysis.
Built with
Editorial notes
Source
- Creator: openai
- Repository: openai/plugins
- Skill file: plugins/ngs-analysis/skills/ngs-dna-germline-variants/SKILL.md
What it does
Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.
Skill instructions
Germline DNA Variants Use this skill for germline WGS, WES, or inherited-disease panel analysis from FASTQ, BAM, or CRAM. If the request is tumor-only, tumor-normal, or low-frequency molecular-barcode panel calling, use a somatic or UMI-panel skill instead. Essential Inputs Confirm: - data type: WGS, WES, or targeted panel - sample model: singleton, cohort, duo, trio, family, or case/control - input type: FASTQ, BAM, or CRAM - organism, reference build, FASTA, indexes, and contig naming - known-sites resources for BQSR, contamination, and annotation - target BED and bait BED for WES/panel data - sex/ploidy assumptions and mitochondrial/sex-chromosome requirements - desired callers, annotation outputs, and final VCF/gVCF expectations Route Prefer nf-core/sarek for full FASTQ/BAM-to-VCF workflows. Use direct GATK4, DeepVariant, samtools, or bcftools only for focused tasks or a custom workflow. Preflight command: bash python plugins/ngs-analysis/scripts/ngspreflight.py --pipeline dnagerml
Explore related resources
Frequently asked questions
What is ngs-dna-germline-variants?
ngs-dna-germline-variants is a open-source AI agent skill with Copy skill directory. Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.
Who is ngs-dna-germline-variants best for?
ngs-dna-germline-variants is best for reusing agent instructions, scripts, and references, data analysis workflows.
How do I install ngs-dna-germline-variants?
Install or run ngs-dna-germline-variants using Copy skill directory. Check ngs-dna-germline-variants for the latest setup command.
Is ngs-dna-germline-variants actively maintained?
ngs-dna-germline-variants may need a closer maintenance check before production use.
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