best way to separate copy number variations from VCF files

Question

[soleimani_homa]

Hi

I am interested in finding copy number variation in my samples. I have raw VCF files. I have looked at the previous questions, but I have not gotten one clear answer. Is there a walker to find CNV's (duplications or deletions) in GATK from raw VCF files?

Hope to hear from you soon.

Regards Homa

[cpad0112]

snpsift?

Answer 1

[WouterDeCoster]

What about using grep? I'd use something like:

cat <(grep '^#' myvariants.vcf) <(grep '<DEL>\|<DUP>' myvariants.vcf) > cnvs.vcf

But I'm not sure how your vcf looks like. The first grep takes the header lines, the second grep searchs for variants containing either the word <del> or the word <dup>.

[soleimani_homa]

Thanks a lot for the reply

Since my VCF files are derived from the GATK software, I would prefer to continue the path with the GATK. Do you have any suggestions for separating the CNVs from the VCF file using GATK?

[ATpoint]

Please do not make the mistake of overcomplicating things. This is a simple pattern-extraction task. Even if you use a GATK filtering tool (if that exists, I don't know) it will do the exact same thing, just wrapped in a GATK_filter_whatever.jar. The suggested solution is perfectly fine.