Extract the DP from VCF file along with the chromosome postion and alteration
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Entering edit mode
5 weeks ago

Hi, I would like to extract the DP 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 INFO

chr1 8004518 . A G 692.77 . 90

DP vcf • 310 views
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1
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use the following command

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

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1
Entering edit mode
5 weeks ago

use bcftools query

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

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1
Entering edit mode
5 weeks ago

paste <(grep -v "^#" YourVCF | cut -f-5) <(grep -v "^#" YourVCF | cut -f10-| cut -d ":" -f3) | sed '1i chr\tstart\tend\tref\talt\tDP' > output

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