Extract the DP and AD from VCF file along with the chromosome postion and alteration

Question

[manojkumarbioinfo]

Hi, I would like to extract the DP and AD from my VCF file, along with the chromosome position and alteration

Example VCF file

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRRS1

chr1 8004518 . A G 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.550;ClippingRankSum=0.000;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.87;ReadPosRankSum=0.521;SOR=0.703 GT:AD:DP:GQ:PL 0/1:49,39:88:99:721,0,1038

Desired Output

CHROM POS ID REF ALT QUAL FILTER DP AD

chr1 8004518 . A G 692.77 . 90 49,39

I can able to extract DP tag using bcftools but cant able to extract AD

bcftools query -f '%CHROM %POS %REF %ALT %DP\n' You.vcf > output.tsv

Answer 1

[Pierre Lindenbaum]

use [] to loop over the genotypes

bcftools query -f '%CHROM %POS [ %AD %DP]\n' in.vcf

[manojkumarbioinfo]

Thank you, but I also tried with awk you can check it out

Answer 2

[manojkumarbioinfo]

By using awk

paste <(grep -v "^#" input.vcf | cut -f-5) <(grep -v "^#" input.vcf | cut -f10-| cut -d ":" -f2,3) |sed 's/:/\t/g' | sed '1i chr\tstart\tend\tref\talt\tNormal_DP\tAltered_DP\tDP'| awk 'BEGIN{FS=OFS="\t"}{sub(/,/,"\t",$6);print}' > output.tsv