Question: how to interpret imputed/phased VCF?
gravatar for mbk0asis
2.3 years ago by
Korea, Republic Of
mbk0asis570 wrote:

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!

phased imputed vcf • 1.0k views
ADD COMMENTlink written 2.3 years ago by mbk0asis570

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 written 2.3 years ago by _r_am31k
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