Answers.Body: <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>
  
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Answers.Text: Yes, I used bcftools +dosage function to extract the GP field only. thank you.
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Answers.CreationDate: 2022-01-16T12:06:05.853Z
Answers.LastActivityDate: 2022-01-16T12:06:05.853Z
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Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-16T01:09:14.390Z
Comments.Text: Does this answer your question? [edit dosage file for various columns](https://bioinformatics.stackexchange.com/questions/18328/edit-dosage-file-for-various-columns)
Comments.UserDisplayName: user324810
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-17T18:50:39.127Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <vcf><snp><genotyping><imputation><chromosomes>
Title: imputed dosage values for vcf files
ThreadText: # imputed dosage values for vcf files
  
  (Asked by: username_0 on 2022-01-14)
  
  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.
  
  **Tags:** vcf, snp, genotyping, imputation, chromosomes
  
  > **Comments:**
  > **username_1**: Does this answer your question? [edit dosage file for various columns](https://bioinformatics.stackexchange.com/questions/18328/edit-dosage-file-for-various-columns)  
  > **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-01-16. Score: 1 | Accepted answer
  
  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>
  
  > **Comments:**
  > **username_0**: Yes, I used bcftools +dosage function to extract the GP field only. thank you.  
  
  ---
  
  