extract sample DP values from VCF

Question

[Ana]

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!

[Ana]

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?

[WouterDeCoster]

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

[Santosh Anand]

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

[noeD]

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

Answer 1

[422385366]

vcftools --geno-depth； You can have a try.

Answer 2

[noeD]

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]'

Answer 3

[b.bearmi]

cat file.vcf | awk -F  ":" '/1/ {print $2}' > DP.values.from.vcf.file