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7.5 years ago
Ana
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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!
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?
Please use
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to reply to earlier answers, as such this thread remains logically structured and easy to follow.The Error says that you may not use
--geno-depth
and--recode
at the same time. Try using one after other.are you able to use R? I did the same with R script