Germline CNV caller

Question

[Samarth Kulshrestha]

Hi,

I am interested in germline CNV events for my Cancer data. So can anyone suggest me any germline CNV caller for Whole genome Sequencing data.

Thanks

[Samarth Kulshrestha]

Thanks Etal for your valuable suggestions. I too explored CNVnator as being used in some of studies. Let me see if CNVnator works for me or not.

Answer 1

[Eric T.]

CNVnator has been used successfully in some studies for analyzing whole-genome germline samples.

Also consider a more general structural variant caller like LUMPY. While you're at it, if you try multiple callers you can use MetaSV to derive a consensus set of structural variant calls.