Project cohort genotype data onto the SGDP reference panel for ancestry PCA.
npx skills add https://github.com/ClawBio/ClawBio --skill claw-ancestry-pca
Please help me install this Agent Skill. Skill: claw-ancestry-pca Source: https://github.com/ClawBio/ClawBio/tree/main/skills/claw-ancestry-pca Command: npx skills add https://github.com/ClawBio/ClawBio --skill claw-ancestry-pca
This Skill places a study cohort into global genetic context by computing a joint PCA against a curated global reference panel and automating the complex preprocessing steps required for robust ancestry inference and reproducible reporting.
Run the ancestry PCA pipeline on your cohort VCF and population map and save the report to a results directory.
High-intent search queries and answers about installing and using this skill.
Ancestry PCA projects VCF genotype data onto the Simons Genome Diversity Project reference panel. It automates contig normalization, extracts shared biallelic SNPs, removes IBD-related samples, and mean-imputes missing genotypes for PLINK merging.
Visualize global population structure using a multi-panel PCA composite figure showing PC1vPC2, PC2vPC3, PC1vPC3, and a scree plot. This Skill generates publication-ready figures alongside CSV tables of PC coordinates and variance.
Preprocessing VCF files is handled automatically before population genetics PCA. The pipeline normalizes contig names, matches common biallelic SNPs, removes related individuals via IBD checks, and mean-imputes missing genotypes.
PLINK works with VCF data for ancestry decomposition by merging cohort genotypes with the SGDP reference panel. The pipeline handles contig normalization and missing genotype imputation to ensure PLINK-compatible joint PCA.
Assign likely population labels by projecting study participants onto global ancestry axes computed from the SGDP reference panel. PC coordinates place cohorts in global context for downstream population assignment and quality control.
Ancestry PCA requires removing related individuals because IBD sharing skews principal components and distorts global population structure. The pipeline detects related samples via IBD checks and excludes them before computing PC coordinates.
MubasherMohammedAnalyze population genetic structure with PCA against SGDP data.
jiaxiaojunQAQGenerate publication-ready clinical decision support documents with GRADE evidence grading and statistical analyses.
zongtingweiGenerates phased and imputed genotypes from VCF data using reference panels and Python tools.
exon-researchProject genome data onto 1000 Genomes reference panels for ancestry analysis.
