Question: Germline CNV caller
0
gravatar for Samarth Kulshrestha
4.1 years ago by
India
Samarth Kulshrestha200 wrote:

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 

sequencing cnv myposts next-gen • 2.6k views
ADD COMMENTlink modified 4.0 years ago • written 4.1 years ago by Samarth Kulshrestha200

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.

ADD REPLYlink modified 9 days ago by RamRS25k • written 4.0 years ago by Samarth Kulshrestha200
0
gravatar for Eric T.
4.1 years ago by
Eric T.2.5k
San Francisco, CA
Eric T.2.5k wrote:

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.

ADD COMMENTlink modified 9 days ago by RamRS25k • written 4.1 years ago by Eric T.2.5k
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