Selection Statistics

Detect natural selection signatures using diversity statistics and extended haplotype homozygosity.

Fst - Population Differentiation

scikit-allel

import allel
import numpy as np

callset = allel.read_vcf('data.vcf.gz')
gt = allel.GenotypeArray(callset['calldata/GT'])
pos = callset['variants/POS']

subpops = {'pop1': [0, 1, 2, 3, 4], 'pop2': [5, 6, 7, 8, 9]}
ac_subpops = gt.count_alleles_subpops(subpops)