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imputed dosage values for vcf files

Hello,

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

It's 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 possesses. 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

vcf genotype predixcan dosage
• 2,307 views • link
updated by Ram Ram • written by rheab1230 • rheab1230

This is what I have tried so far.

I tried to remove the brackets using this command and it worked.

sed -e 's/\[[^][]*\]//g'

And for adding the 22_!605149_T_C I did this:

awk '{ID=$1"*"$2"* "$3"*"$4"* " +b37; print ID}' genotype.chr22_1.txt > genotype.chr22_2.txt

But it just gives me a separate file with these values and not want I want. I tried to join the columns using R but it doesn't generate a separate column. the command used is:

genotype_chr22_1$ID <- paste(genotype_chr22_1$CHROM, genotype_chr22_1$POS,genotype_chr22_1$REF, genotype_chr22_1$ALT, sep = "_")
• 0 views • link
updated by Ram Ram • written by rheab1230 • rheab1230 
cat <( \
      paste -d '\t' \
         <(echo "Id") \
         <(head -1 test.tsv \
      | cut -f5- \
      | sed -e '$s/\[[[:digit:]]\+\]//g; s/_HG[[:digit:]]\+//g') ) \
    <( \
      paste -d '\t' \
        <(awk 'NR>1 {print $1"_"$2"_"$3"_"$4"_b37"}' test.tsv) \
        <(awk 'NR>1 {print $0}' test.tsv | cut -f5- | sed 's/\.[[:digit:]]\+//g')) \
> output.tsv

I used this command to get the desired output.

• 0 views • link
updated by Ram Ram • written by rheab1230 • rheab1230

Also to extract the dosage values from the above file after running michigan imputation server. I used bcftools +dosage function.

• 0 views • link
updated by Ram Ram • written by rheab1230 • rheab1230

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