Detection of CNVs from vcf file

Question

[misbahabas]

Aslam o Alikum

I am beginner in this field, I have vcf files of DOG genome data. Now,I want to detect CNVs from these files.Please tell me how to do this or is there any tool which detect CNVs from vcf files?? please tell me if anyone know.

Thanks in advance

Answer 1

[Devon Ryan]

Detecting CNVs from a VCF file would be what we call "a fool's errand". You'll want to use the BAM files instead. You can find appropriate tools if you google "CNV detection".

[brentp]

on the other hand, the benefit of the VCF over coverage-only methods is that you know the allele-balance. If the DP is high for a few variants and those same variants show an allele-balance (e.g. alt / ref+alt) of 0.66 or 0.33, then you can be fairly confident it's a CNV.

Answer 2

[d-cameron]

You should only consider this if you cannot get access to the bam files.

The only tool I know of that performs what you're requesting is VCF2CNA http://biorxiv.org/content/early/2017/04/26/131235. I have not used it personally so I cannot vouch that is actually works as advertised.

Answer 3

[talalamin]

If you have bam files do not detect CVN from VCF files.