Running CODEX2 on WGS data

[Migle Gabrielaite]

Dear CODEX2 Authors,

I would like to use your tool to call CNVs on WGS data. However, the tutorial only covers how to run the tool on WES data. Should the WGS data analyzed the same way as WES? or should the different recommendations be followed?

Best,

Migle

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[Yuchao Jiang]

Hi Migle,

Yes CODEX2 is primarily for WES and targeted sequencing. For WGS, I think you can start with 5kb consecutive windows (the size depends on your sequencing depth but I think 5kb is a good start). That is, generate bed file with each row corresponding to a 5kb window along the genome.

Hope that this helps,

Yuchao

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