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?