text: user14859: 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.
  
  user492: When i was still working in the field of genotype imputation, a dosage was the expectation (average) of the (posterior) genotype probabilities, coded as GP in the OP's VCF. I once contributed code to bcftools to convert genotype probabilities stored in the GP field to dosages. It looks like that code may now live in a bcftools plugin called "dosage": https://samtools.github.io/bcftools/howtos/plugins.html
  
original_text: 14859: <p>I have one more question related to genotype file. I submitted the job in michigan imputation server.</p>
  <p>and my imputed dosage for chr 22 file is:</p>
  <blockquote>
  <p>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</p>
  </blockquote>
  <p>Its coming like this.</p>
  <p>wherein the test data provided in your predixcan tutorial looks like this:</p>
  <blockquote>
  <p>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</p>
  </blockquote>
  <p>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.</p>
   492: <p>When i was still working in the field of genotype imputation, a dosage was the expectation (average) of the (posterior) genotype probabilities, coded as GP in the OP's VCF. I once contributed code to bcftools to convert genotype probabilities stored in the GP field to dosages. It looks like that code may now live in a bcftools plugin called &quot;dosage&quot;: <a href="https://samtools.github.io/bcftools/howtos/plugins.html" rel="nofollow noreferrer">https://samtools.github.io/bcftools/howtos/plugins.html</a></p>
  