ArrayIndexOutOfBoundsException

Not sure if this is helpful, but I ran into the same issue on 0.2.27. I tried to show chromosome 7 after running variant qc, and it showed chromosome 6.

yeah, haven’t figured out what’s going on yet. This does seem quite bad. We need to replicate this in a dev environment

OK, we haven’t figured out what was causing it, but apparently the issue only manifested on files written with versions of Hail around 0.2.19-0.2.20. It’s fixed here:

We’ll make a release tomorrow.