Hello everyone,

I'm planning to compute genotype likelihoods on ANGSD (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0356-4) and then use the resulting beagle file as input for other softwares such as NgsAdmix and PCAngsd. There are a few filters I'd like to apply to the admixture and pca analysis (such as minMaf and minInd. However, these filters can be set both in ANGSD and also on ngasadmix and pcangsd, so I was wondering when should I set these filters. I believe I should rather set them for pcangsd and ngsadmix, once I already have the genotype likelihood files. Or is there a way that these parameter affects the computation of the genotype likelihoods on angsd?

I hope I made myself clear,

Cheers