GQ set to NA when PL is NA after split_multi_hts

Hail Query & hailctl
1

Hello,

One of our VCFs is delivered with GQs but without PLs at homref sites. We just saw that if split_multi_hts is used on a MatrixTable where some entries have a PL set to NA, those entries GQ fields are then set to NA. Is this expected behavior?

Thank you,
Mike

2

Hey @mwilson, what version of Hail are you using?

3

Hi Dan, I saw this in version 0.2.24 and 0.2.27.

4

@mwilson, thanks for the report, we are looking into it right now.

5

Thanks for bringing it to our attention! I’ve PRed a fix here: https://github.com/hail-is/hail/pull/7571

We’ll let you know when we’ve deployed a version with the fix.