I've recently noticed that the -minInd filter in ANGSD is not working properly. For example, using -minInd 76 on a test run gives a MAF file:
chromo position major minor ref knownEM pK-EM nInd
chr10 90625430 C G C 0.135223 0.000000e+00 76
chr10 90625447 G A G 0.031195 1.791576e-10 75
chr10 90625462 C A A 0.319601 0.000000e+00 76
I've recently noticed that the
-minInd
filter in ANGSD is not working properly. For example, using-minInd 76
on a test run gives a MAF file:chromo position major minor ref knownEM pK-EM nInd chr10 90625430 C G C 0.135223 0.000000e+00 76 chr10 90625447 G A G 0.031195 1.791576e-10 75 chr10 90625462 C A A 0.319601 0.000000e+00 76
best,