Is it possible to detect CNV without having a reference control group/sample?

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2.5 years ago

Waly • 0

Hi, I'm trying to detect CNV from NGS data. I understand that there are many CNV detection methods published and freely available. My question is; is it a must to define a control group (reference) for detecting CNV in a query sample? I'd be very surprise to get a NO answer, and looking forward learning about such and tool .. Thanks!

CNV aneuploidy • 1.0k views

ADD COMMENT • link updated 2.5 years ago by brunobsouzaa ▴ 830 • written 2.5 years ago by Waly • 0

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You can use cnvkit, it allows you to build a flat reference from your reference genome file.

ADD REPLY • link 2.5 years ago by brunobsouzaa ▴ 830

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yes: DELLY2, SMOOVE....

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 161k

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many thanks for suggesting; if I used DELLY; where to get this hg38.map file? I don't see that in their file list: Mappability Maps ;

One last question: is it reliable to have CNV calls, and Aneuploidy interpretations based on analysis that lacks a control? and is just based on read-depth profiles?

ADD REPLY • link 2.5 years ago by Waly • 0

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