CNV calling on WGS only on gene positions

Question

[pabloatienzalo]

Hello,

I would like to perform a CNV calling on WGS samples from Maize only on gene's positions. For that, I have created a script using the genes as target and the batch command. However, the final segments are too large, over 1Mb and the callings are not specific to the positions of the genes.

We would like to call the CNVs only in the target regions. The reference genome used is soft masked.

Here you can find the script used for the workflow:

cnvkit.py batch file.bam -n -m wgs -f softmasked.fa --targets Genes.bed

¿Could you offer some recommendations to perform the calling for our needs?

Thank you very much in advance

[igor]

Why not do the standard CNV analysis and then overlap with the genes?