Calling CNVs from SNPs within targeted gene panel
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.
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kate.imo.glennon •
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I work with targeted sequencing and I like to use
cnvkitandExomeDepthfor CNV calls. Take a look into their respective manuals, might help you!convadingis also a good tool, but it's too slow!Thanks! I typically use CNVkit but I was looking for something that isn't read count based.