Analysis

snputils includes analysis routines for dimensionality reduction, allele frequencies, population-genetic statistics, admixture mapping, and simulation.

PCA and Ancestry-Aware Embeddings

from snputils.processing import PCA, mdPCA, maasMDS

pca = PCA(n_components=2)
coords = pca.fit_transform(snpobj)

mdPCA handles missing data, and maasMDS uses local ancestry masks for ancestry-specific multidimensional scaling.

Allele Frequencies and F-Statistics

from snputils.stats import allele_freq_stream, fst, f2, f3, f4, d_stat

freq = allele_freq_stream("cohort.pgen", chunk_size=50_000)

The statistics module supports D, f2, f3, f4, f4-ratio, and FST with jackknife standard errors where applicable.

Command-Line Tools

The package installs a snputils command with analysis-oriented subcommands. Run:

snputils --help