domains / families / science / population-structure

population-structure

separate

Infers and describes population structure with PCA (plink2 --pca, smartpca/EIGENSOFT, FlashPCA2), model-based clustering (ADMIXTURE, fastSTRUCTURE), FST estimators (Weir-Cockerham vs Hudson), and f-statistics (f3/f4/D via AdmixTools/admixr), plus Python plotting of PCs and Q barplots. Every output is a model-conditioned description of variance, not truth: PCs conflate ancestry with LD/inversions/relatedness/batch, ADMIXTURE Q-values are panel- and K-dependent artifacts, and CV-minimum K is a guide not the true population count. FST must combine SNPs as a ratio of averages (sum numerators / sum denominators), never an average of per-SNP FST; negative per-SNP FST is normal and must not be clamped. f3/f4/D need a block jackknife or the significance is fake. Use when running PCA, ADMIXTURE, FST, or f-statistics on QC'd genotypes. For QC and KING relatedness see plink-basics; for LD pruning see linkage-disequilibrium; for array-based Python pipelines see scikit-allel-analysis.

When to use

• running PCA
• ADMIXTURE clustering
• FST estimation
• f-statistics analysis
• Python plotting of PCs
• Q barplots
• model-based clustering
• population structure inference

When not to use

• QC and KING relatedness
• LD pruning
• array-based Python pipelines
• phased haplotype work
• introgression detection

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