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United KingdomMember Posts: 404 ✭✭✭

"The ... rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles."

I have quite a few sites for which MQRankSum and ReadPosRankSum are missing. How does VariantRecalibrator handle this missing information?

Tagged:

Hi Tommy,

That's a good question, I'm not sure. I expect it just skips that dimension for the variant in question but I don't know how this affects the variant's ranking overall. Unfortunately the one person who knows the model in and out (Ryan Poplin, @rpoplin) is on vacation; I'll see if someone else knows but it may be a while before I can get you an answer.

Geraldine Van der Auwera, PhD

• United KingdomMember Posts: 404 ✭✭✭

Thanks @pdexheimer and @Geraldine_VdAuwera. I wonder what "marginalizing over a dimension via sampling" exactly means, but happy to know, that it has been attended to by @rpoplin. I guess I have to look at the code, if I want further details. I thought maybe missing values would have been imputed somehow or alternatively just set equal to the mean or median. Thanks.