I need some help for the LOH in the output of CNVkit. How could I get the region of LOH for SciClone analysis? In the documentation I only find how to plot the LOH, and I'd like to get the detail information of these region.
If you run the call sub-command with a VCF (see here), the output .cns file is a table with the columns cn1 and cn2. You can filter the rows for columns where cn1 != cn2 with awk, Excel, cnvlib, or any tool you like to get the segments with allelic imbalance. Those are the rows that are informative for SciClone analysis, I think.