Hi, hope all is well. I’m working on the AllofUs platform to calculate some PRS. I’m using a custom code and Hail MT for calculations, which is working but is time-consuming and expensive. A part of the code is subsetting the variants in the PRS weights df from the MT, and I came across @tpoterba …

What code are you using to show the genotypes? vds.variant_data.GT.show() shows only the variant data. The VDS is a split representation: reference data and variant data are stored separately, each on in its own Hail Matrix Table: vds.reference_data and vds.variant_data. If, for your analysis, you …

Hi @danking , thank you for your response! Yes, I used vds.variant_data.GT.show() to show the genotypes. [image] danking: If, for your analysis, you need reference information (in particular, if you need to decide if a given sample is a confident homozygous reference call instead of a no call) …

Does that mean an NA could either be a nocall or a homozygous reference? Yes, that’s exactly what NA means. The reference data is not stored row-by-row. The reference data is stored like a GVCF: there are “reference blocks” which implicitly span multiple rows. Is it safe to assume that the var…

Great! Thank you so much, Dan. I appreciate the help!

Hi @danking , sorry to keep bugging you with this but I have a follow-up question. I’m trying to understand how Hail treats the missing calls. When using mt.GT.show I could see the missing calls as NA: [image] But when using hl.is_missing, they are still NA instead of True I guess: [image] Same…

'GT' are present in MT but missing from VDS for same samples

Hail Query & hailctl

danking October 4, 2023, 2:39pm 7

Hey! Sorry for the delay, I answered in your other question How does Hail treat missing calls?

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'GT' are present in MT but missing from VDS for same samples

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