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HLA prediction quality #11

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rcanovas opened this issue Jul 6, 2020 · 1 comment
Open

HLA prediction quality #11

rcanovas opened this issue Jul 6, 2020 · 1 comment

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@rcanovas
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rcanovas commented Jul 6, 2020

Is there any way to obtain the quality (r2 or INFO) of imputing HLA-* ?
So far, after doing the prediction I can only see the alleles and only one probability.
@zhengxwen
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Use that probability for a pair of alleles, and a threshold 0.5.
Or output all prob. of the full pairs of alleles,

hlaPredict(object, snp, type="prob")

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@rcanovas @zhengxwen