Brent Pedersen

actually, I don't think that should affect what you are reporting here. You can try updating to cyvcf2 v0.9.0 to see if that resolves it, but I don't think it...

It could, but it uses those sites for the heterozygosity stuff too, so the only thing left would be the sex plots.

I'm wary of writing software that catches all possible problems and gives a 0 exit code. I'm not completely against what you're saying, but I'm not sure how to implement....

a la picard check bam id.

I wonder if you are getting a mix of peddy modules. the new version has a different set of sites and so maybe you're somehow getting the old PCA module?...

you must have a very old version of scikit-learn. I would update that, re-run and report the error (if there is one).

there is no way to specify this, but you should just see those samples as having relatedness of 1 in the output.

I'll accept a pull request for this. Pretty sure I've been using peddy on python3, but I no longer no much about all these packaging issues.

hi, this is fixed in master, it happens due to deprecated use of `ix`. But master has conflicts in conda which I don't know how to fix. You can clone...

yes, it's possible, but this doesn't appear to be failing on the sex check part.