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Germline CNV caller

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

cnv next-gen-sequencing
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updated by Ram Ram • written by Samarth Kulshrestha 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.

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updated by Ram Ram • written by Samarth Kulshrestha Samarth Kulshrestha

1 answer

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.

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updated by Ram Ram • written by Eric T. Eric T.

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