Whole Exome Sequencing Depth

Question

[bioinfonerd]

Hi,

I want to calculate Copy number variations(CNV) from Whole exome seq data. What is the correct sequencing depth that can result in correct identification of CNVs.

Also is it possible to extract somatic CNVs without matched tumor normal?

Thanks.

[Ram]

Somatic CNVs are usually called CNAs (aberrations). Identifying differences between tumor and normal cells along any omics dimension needs normal cells for the comparison.

[gab]

Sequencing depth per se is not a key parameter, what is really important is the difference in read depth between normal and tumor samples, so you really should have both. A minimum value of depth is set to avoid false positives/negatives during calculations, usually it is a default parameter in tools, but you can adjust it.