BEAGLE format?
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kellybarr commented
I've been futilely trying to run and ngsDist analysis. The BEAGLE file I'm using is made with this command:
angsd -P 8 -b my_list -ref my_ref -anc my_anc -out my_out -uniqueOnly 1 -remove_bads 1 -only_proper_pairs 1 -trim 0 -C 50 -baq 1 -minMapQ 20 -minQ 20 -minInd 50 -setMinDepth 25 -setMaxDepth 400 -doCounts 1 -GL 1 -doMajorMinor 1 -doMaf 1 -skipTriallelic 1 -doGlf 2 -doGeno 32 -doPost 1 -SNP_pval 1e-6
Do you see any issues?
fgvieira commented
Dear @kellybarr,
not sure what you are trying to do but, from your command it seems you are calculating genotype posterior probabilities, not likelihoods.
Even though ngsDist will work with prob, it has only been tested with likelihoods.