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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.

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  • $\begingroup$ Does this answer your question? edit dosage file for various columns $\endgroup$
    – user324810
    Jan 16, 2022 at 1:09
  • $\begingroup$ 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. $\endgroup$
    – Community Bot
    Jan 17, 2022 at 18:50

1 Answer 1

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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

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  • $\begingroup$ Yes, I used bcftools +dosage function to extract the GP field only. thank you. $\endgroup$
    – Rhea Bedi
    Jan 18, 2022 at 18:32

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