Calling CNVs from SNPs within targeted gene panel

Question

[kate.imo.glennon]

Hi there! I have targeted sequencing data from a custom gene panel and am comparing different methods of calling CNVs.

Is there a good way to call CNVs from SNPs within the targeted genes? Most callers that I've seen depend on SNP arrays. I understand that coverage based callers will likely perform better, but for the purpose of my research I am trying to compare SNP based vs coverage based CNV calling within my targeted panel.

I'd appreciate any program suggestions or opinions on the best way to approach this.

[brunobsouzaa]

I work with targeted sequencing and I like to use cnvkit and ExomeDepth for CNV calls. Take a look into their respective manuals, might help you! convading is also a good tool, but it's too slow!

[kate.imo.glennon]

Thanks! I typically use CNVkit but I was looking for something that isn't read count based.