Seperate Log2 ratio

[pcr876]

Hi,

Thank you for the wonderful tool ! I am using CNVkit on targeted sequencing data(Nanopore) for copy number loss/gain of genes. I have known CNVs, for some genes my sample has homozygous and heterozygous deletion of genes. For example, for CDKN2A and CDKN2B genes, one of my samples has heterozygous deletion of CDKN2A and homozygous deletion for CDKN2B. So ideally the log2 ratio should be very low for CDKN2B. But in .cns file, it merges all the values based on chromosome so when I do scattered plotting, the segmented line is at the same value. I want to see separate values for both genes to call it as hetero or homo.

How can I do that?

Shreya

[etal]

Since CDKN2A and CDKN2B overlap in the genome, you won't be able to separate them completely. But if you plot both genes with the scatter command, you should be able to see what's going on there by looking at the dark gray points. You can also use the genemetrics command to get the average log2 ratio within each gene, based on segments or raw bins.