Best way to detect CNV using WGS data

Question

[JellyFrog]

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!

Answer 1

[Pierre Lindenbaum]

manta, delly2, smoove....

[JellyFrog]

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

Answer 2

[colindaven]

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.

[Pierre Lindenbaum]

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

I think OP is asking for WGS data.