How to call CNV without normal samples

Question

[SkyL]

Hi,

I wonder if it is possible to detect somatic copy number variation without normal samples? As far as I can remember is that most of the tools take into the normal.BAM and tumor.BAM and they compare the read count for the targeted region and that ratio can be used to infer CNV. However, if there's no normal.BAM at all, is it still possible to call CNV from the tumor.BAM? Thanks!

[ivivek_ngs]

There is no straightforward way to answer this but often I have seen Panel of Normals (PON) being used for such. Check this thread from Kevin Blighe. Might be of help. Copy number events can be called from the data but somatic without a reference is always tricky.

Answer 1

[abedkurdi10]

You can use cnvkit tool to call somatic CNVs. Don't forget to use --drop-low-coverage argument too.

[garcesj]

https://cnvkit.readthedocs.io/en/stable/germline.html