imputed dosage values for vcf files

Question

[rheab1230]

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

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.

[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 = "_")

[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.

[rheab1230]

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