bio-population-genetics-selection-statistics
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)
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