Detecting copy number variants from whole-exome sequencing data

Question

[Shicheng Guo]

Hi All,

1. Which tool could provide the most accurate CNV calling to whole-exome sequencing data?
2. Is there any publicly available data have both WGS and WEX to the same sample to be used for CNV calling evaluation.

Thanks.

[WouterDeCoster]

Probably better to use long read sequencing as truth set rather than short read wgs. Or maybe both.

[hafiz.talhamalik]

as suggested earlier CNVkit is a very good and easy to use tool. I aslo recommend that

Answer 1

[jared.andrews07]

1. I've really enjoyed CNVkit. It's very easy to use, has good visualizations, and good documentation. "Accuracy" is a hard thing to measure for copy number calling if interested in focal changes as well, but the results from it make sense and correspond with other methods I've used, like copyCat.
2. 1000 Genomes has some samples with both.