Individual skill
wgs-prs
End-to-end WGS to polygenic risk score pipeline. Takes paired-end FASTQ files (or a pre-existing VCF) through nf-core/sarek for variant calling, applies VCF QC (normalisation, hard filtering, Ti/Tv and Het/Hom checks), then computes polygenic risk scores via the PGS Catalog. Fills the FASTQ to VCF gap upstream of the gwas-prs skill.
skills/wgs-prs/SKILL.md
Source commit df61706c3e32fea21ad88f5b8a5189c895f9524d
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- No
- Repository scan complete
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- Skill scan complete
- No
- Observed behavior
- Not checked yet
- Last checked
- Nov 8, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
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Repository context
- Repository stars (not skill ratings)
- 1,176
- Repository last updated
- Nov 8, 2026
- License
- NOASSERTION
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-agents Repository topic
- bioinformatics Repository topic
- equity Repository topic
- genomics Repository topic
- local-first Repository topic
- openclaw Repository topic
- population-genetics Repository topic
- reproducibility Repository topic
- wgs Declared skill tag
- whole-genome-sequencing Declared skill tag
- polygenic-risk-scores Declared skill tag
- prs Declared skill tag
- sarek Declared skill tag
- nf-core Declared skill tag
- nextflow Declared skill tag
- variant-calling Declared skill tag
- vcf-qc Declared skill tag
- gatk Declared skill tag
- engineering Derived category
- testing Derived category
- testing-browser Derived category
Declared tags are partial or unavailable.
Files and excerpt
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Browse files
SKILL.mdcore · 13,059 bytesSKILL.mdcore · 13,059 bytesSKILL.mdcore · 13,059 bytestests/test_repro_bundle.pyruns · 15,693 bytestests/test_sarek.pyruns · 6,304 bytestests/test_vcf_qc.pyruns · 11,887 bytestests/test_wgs_prs.pyruns · 12,926 byteswgs_prs.pyruns · 29,073 byteswgs_prs_repro_bundle.pyruns · 10,066 bytes
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