I have one more question related to genotype file. I submitted the job in michigan imputation server.
and my imputed dosage for chr 22 file is:
22 16050435 22:16050435:T:C T C . PASS AF=0.00098;MAF=0.00098;R2=0.23769;IMPUTED GT:DS:HDS:GP 0|0:0.002:0.001,0.000:0.998,0.002,0.000 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0.001:0.000,0.001:0.999,0.001,0.000 0|0:0:0,0:1,0,0 0|0:0.001:0.001,0.000:0.999,0.001,0.000 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0.001:0.001,0.000:0.999,0.001,0.000 0|0:0.002:0.000,0.002:0.998,0.002,0.000 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0.001:0.000,0.001:0.999,0.001,0.000 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0.002:0.000,0.002:0.998,0.002,0.000 0|0:0:0,0:1,0,0 0|0:0.001:0.001,0.000:0.999,0.001,0.000 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0 0|0:0:0,0:1,0,0
Its coming like this.
wherein the test data provided in your predixcan tutorial looks like this:
22_16494187_C_A_b37 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
Also it states that the imputed dosage should be encoded on a 0-2 scale representing the number imputed or number of the effect alleles the sample posseses. Do anyone know should I convert my vcf files to the desired input genotype file to train the model. I don't understand in my vcf files which column is representing dosage values Thank you.