# GQ set to NA when PL is NA after split\_multi\_hts

**URL:** <https://discuss.hail.is/t/gq-set-to-na-when-pl-is-na-after-split-multi-hts/1181>\
**Category:** Hail Query & hailctl\
**Created:** [November 20, 2019, 7:30pm UTC](https://discuss.hail.is/t/gq-set-to-na-when-pl-is-na-after-split-multi-hts/1181 "2019-11-20T19:30:13Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![mwilson](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/mwilson/32/376_2.png) [@mwilson](https://discuss.hail.is/u/mwilson)\
**Post date:** [November 20, 2019, 7:30pm UTC](https://discuss.hail.is/t/gq-set-to-na-when-pl-is-na-after-split-multi-hts/1181/1 "2019-11-20T19:30:13Z")

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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

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**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [November 20, 2019, 7:33pm UTC](https://discuss.hail.is/t/gq-set-to-na-when-pl-is-na-after-split-multi-hts/1181/2 "2019-11-20T19:33:12Z")

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

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**Author:** ![mwilson](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/mwilson/32/376_2.png) [@mwilson](https://discuss.hail.is/u/mwilson)\
**Post date:** [November 20, 2019, 7:34pm UTC](https://discuss.hail.is/t/gq-set-to-na-when-pl-is-na-after-split-multi-hts/1181/3 "2019-11-20T19:34:06Z")

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

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**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [November 20, 2019, 7:40pm UTC](https://discuss.hail.is/t/gq-set-to-na-when-pl-is-na-after-split-multi-hts/1181/4 "2019-11-20T19:40:11Z")

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

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**Author:** ![wang](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/wang/32/146_2.png) [@wang](https://discuss.hail.is/u/wang)\
**Post date:** [November 20, 2019, 7:51pm UTC](https://discuss.hail.is/t/gq-set-to-na-when-pl-is-na-after-split-multi-hts/1181/5 "2019-11-20T19:51:37Z")

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

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