Scikit Allel Analysis

In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (pi, theta, Tajima's D), SFS, FST (Weir-Cockerham, Hudson, Patterson), f3/D admixture stats, LD pruning, PCA, and selection scans (iHS, XP-EHH, nSL, Garud H). Nearly every statistic is a ratio or density with one silent denominator bug in two faces: omit is_accessible= and per-base pi/theta divide by total span not accessible bp (deflated 2-5x); average per-SNP FST instead of sum(a)/(sum(a)+sum(b)+sum(c)) and the estimate is rare-variant-biased - scikit-allel returns the (a,b,c) and (num,den) components on purpose to force ratio-of-sums. to_n_alt default fill…