Entering edit mode
5.7 years ago
mbk0asis
▴
680
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!
The header should have some annotation metadata on the IMP2, or at least the IMPUTE2 tool documentation should, if not the VCF header.