convert genipe *imput2 to plink format

Question

[panmy2015]

Dear All,

I am running imputation with genipe tools now, it is very nice and friendly which combine plink-shapeit-impute2 in one pipeline. The output file is .impute2 file, my question is I want to convert to plink input format, and I found my genotype rate is lower than it used to be. And this is my final.imput2 file.

03 3:11290122_G_T rs347591 11290122 G T 0.00000 0.81569 0.18431
03 rs1801282 rs1801282 12393125 C G 0.00000 0.00000 1.00000
03 rs2290159 rs2290159 12628920 G C 1.00000 0.00000 0.00000
03 rs6793656 rs6793656 13823342 A G 1.00000 0.00000 0.00000
03 3:14954549_A_C rs12635574 14954549 A C 0.00000 0.00000 1.00000
03 3:14958126_G_A rs11128722 14958126 G A 0.00000 0.00000 1.00000
03 3:20073193_T_A rs189267552 20073193 T A 1.00000 0.00000 0.00000
03 3:20117233_C_T rs4858758 20117233 C T 0.00000 1.00000 0.00000
03 3:27040451_C_A rs67605425 27040451 C A 1.00000 0.00000 0.00000
03 3:27562988_C_T rs2643826 27562988 C T 0.00000 0.00000 1.00000

Another question is *imput2 file is same as *gen file or not? I think one is pruned another one is unpruned. Not sure how to convert them between each other.