# Partially missing genotypes

**URL:** <https://discuss.hail.is/t/partially-missing-genotypes/1169>\
**Category:** Hail Query & hailctl\
**Created:** [November 15, 2019, 8:29pm UTC](https://discuss.hail.is/t/partially-missing-genotypes/1169 "2019-11-15T20:29:39Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![eatkinson](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/eatkinson/32/336_2.png) [@eatkinson](https://discuss.hail.is/u/eatkinson)\
**Post date:** [November 15, 2019, 8:29pm UTC](https://discuss.hail.is/t/partially-missing-genotypes/1169/1 "2019-11-15T20:29:40Z")

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Hi guys,  
I am wondering how Hail treats partially missing genotypes (e.g. 0/.). I am loading in VCF files that have been constructed such that they are haploid for much of the genomes, say 50% or more partially or fully missing varying by individual, and am hoping to run linear regression. For context, plink forces you to treat such calls as either homozygous or reference, and I would like for them to just remain partially missing so as to result in the correct N. Clarity and/or advice appreciated!  
Thanks,  
Elizabeth

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [November 15, 2019, 8:30pm UTC](https://discuss.hail.is/t/partially-missing-genotypes/1169/2 "2019-11-15T20:30:56Z")

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Hail will treat a `./0` or `0/.` as a fully missing genotype in VCF import.

Hail does support haploid calls, which should be represented as `0`.

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**Author:** ![eatkinson](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/eatkinson/32/336_2.png) [@eatkinson](https://discuss.hail.is/u/eatkinson)\
**Post date:** [November 15, 2019, 8:42pm UTC](https://discuss.hail.is/t/partially-missing-genotypes/1169/3 "2019-11-15T20:42:53Z")

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OK great to know. So if I swap out all the partially missing for the non-missing call (0/. -\> 0 or 1/. -\> 1) in the VCF to load in, then things will be happy? Ideally it would be great if phase were retained, but I understand this isn’t implemented yet, so this should work great for unphased efforts.

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [November 15, 2019, 8:47pm UTC](https://discuss.hail.is/t/partially-missing-genotypes/1169/4 "2019-11-15T20:47:57Z")

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you can encode phase separately in the FORMAT field, using another integer for example.

Encoding phase in a haploid call seems like an ill-defined construct, and Hail can’t represent that.