Brent Pedersen

Peddy requires that there is depth information associated with the variants. This is critical for filtering to high-quality genotype calls. You can add this artificially by setting e.g. AD=20,20. Peddy...

It would have to go in your VCF. Peddy only uses the first 6 columns of the ped/fam file to determine the expected relationships.

I have seen this too and haven't found where to fix in the code. I'll make another pass and see if I can resolve. Thanks for reporting.

I'll look into this. Meanwhile, can you give 1905 a fake parent? I think that will give you 0.25 based on the current logic.

your issue aside (but not forgotten) I love seeing peddy use like this!

bumping this as a reminder to myself. this would be good to resolve.

hmm. maybe when there's a single sample we need to use `X[:, np.newaxis]` or something as the number of features should be ~ 20K.

I'll try to carve out some time on friday to work on peddy and get these resolved. thanks for reporting.

I can run with 1 sample on master. It seems like maybe you're only finding a single snp out of the full set. E.g. your log info says `(shape: (2504,...

I see the problem that's causing this. Will release 0.4.2 shortly.