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Question: how to interpret imputed/phased VCF?
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Hi. I have several vcf files contain imputed/phased variant calls download from HipSci.

They say they used IMPUTE2 for imputation, so the files have the information like below.

X       65179   .       G       C       IMP2=0.474,0.864,0.93   GT:GP:PS        0|1:0.061,0.93,0.009:60034
X       65351   .       G       C       IMP2=0.441,0.787,0.881  GT:GP:PS        0|1:0.118,0.881,0:60034
X       65392   .       G       A       IMP2=0.467,0.84,0.916   GT:GP:PS        0|1:0.075,0.916,0.009:60034

I figured out most of the abbreviations such as GT, GP, and PS, but I still don't understand what the "IMP2=" columns tell me.

Can someone help me understand that?

Thank you!

ADD COMMENTlink 19 months ago mbk0asis • 420
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1

The header should have some annotation metadata on the IMP2, or at least the IMPUTE2 tool documentation should, if not the VCF header.

ADD REPLYlink 19 months ago
RamRS
21k

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