aCaMEL/admixpipe
Enhancements & fixes SNPio 1.6.0–1.7.6 counted each homozygote four times when computing minor allele frequencies (btmartin721/SNPio#51). As a result, --min_maf removed loci whose MAF passes the threshold when the minor allele is mostly in heterozygotes. On the test data, 1.0.0 kept 915 of the 1,130 loci that pass the...