Individual skill

plink2-gwas-analysis

GWAS and population genetics tool. Processes PLINK (.bed/.bim/.fam), VCF, and BGEN; runs QC (MAF, HWE, missingness), IBD estimation, PCA, and linear/logistic regression GWAS. Outputs Manhattan-ready summary stats. Use regenie or SAIGE for biobanks (>100k samples) needing mixed models.

skills/genomics-bioinformatics/variant/plink2-gwas-analysis/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

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Last checked

Nov 5, 2026

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