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Best way to detect CNV using WGS data

Hi,

I am new into this field. Could someone please suggest the best way you have used to detect copy number variants from human WGS data?

I did some research online, suggesting to use control-FREEC; CNVkit. Due to lack of experience, I am unable to tell which one works the best.

Any comment is appreciated!

wgs cnv
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written by JellyFrog • JellyFrog

2 answers

manta, delly2, smoove....

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for the quick response, Pierre. Are you suggesting to use solely one tool or a combination of a bit of those.

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written by JellyFrog • JellyFrog

CNVkit was relatively easy and results plausible on a large sample of about 70 exomes I had once. Results were not validated by the users back then though.

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written by colindaven colindaven

CNVKit is designed for use with hybrid capture, including both whole-exome and custom target panels

I think OP is asking for WGS data.

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written by Pierre Lindenbaum Pierre Lindenbaum

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