extract sample DP values from VCF
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7.2 years ago
Ana ▴ 200

I want to extract only sample DP values (the second value in the example below) from my cvf file, this is my genotype annotation

0/0:7:7,0:7:244:0:0:0,-2.10721,-20.8228
0/1:3:3,1:2:74:1:37:-2.76372,0,-3.15643
0/0:9:9,0:9:321:0:0:0,-2.70927,-19.2273
0/0:11:11,0:11:407:0:0:0,-3.31133,-36.8199

How can I do that? can I do that with vcf tools? I would appreciate any suggestion!

vcf perl vcftools • 3.8k views
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Alright, this is my code /data/programs/vcftools_0.1.13/bin/vcftools --vcf my_file.vcf --geno-depth --recode --out results1.vcf

bu I get an error message: Error: Only one output function may be called.

any suggestion for this problem?

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Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow.

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The Error says that you may not use --geno-depth and --recode at the same time. Try using one after other.

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are you able to use R? I did the same with R script

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7.2 years ago
422385366 ▴ 10

vcftools --geno-depth´╝Ť You can have a try.

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7.1 years ago
noeD ▴ 130

if you want you can use R (in my opinion it is the best solution) or bash script, for the second option you have to select the column with that field and the following command will extract the DP:

perl -F: -w 'print $F[1]'
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5.3 years ago
b.bearmi ▴ 10
cat file.vcf | awk -F  ":" '/1/ {print $2}' > DP.values.from.vcf.file
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