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.