I am having issues understanding the columns for SV inputs. It seems like Tumor_Varcount is the number of reads supporting the ALT in the tumor sample, and Tumor_Depth seems like it would be the number of reads supporting the ALT and REF in the tumor sample. If my understanding of both of those is correct, then the Normal_Depth would be the number of reads supporting the ALT and REF in the normal sample -- even though a Normal_Varcount is not required. If that's the case, then I don't understand the purpose of the Normal_Depth, since you can sequence any sample to any depth you want and it wouldn't have a meaningful relationship to the other two columns.
I also couldn't find in the code how or where any of these 3 columns are actually used. Can someone clarify?
I was also wondering if we could use this tool for structural variants where we only have data from one sample, or if there's a minimum number of samples recommended.
I am having issues understanding the columns for SV inputs. It seems like
Tumor_Varcountis the number of reads supporting the ALT in the tumor sample, andTumor_Depthseems like it would be the number of reads supporting the ALT and REF in the tumor sample. If my understanding of both of those is correct, then theNormal_Depthwould be the number of reads supporting the ALT and REF in the normal sample -- even though aNormal_Varcountis not required. If that's the case, then I don't understand the purpose of theNormal_Depth, since you can sequence any sample to any depth you want and it wouldn't have a meaningful relationship to the other two columns.I also couldn't find in the code how or where any of these 3 columns are actually used. Can someone clarify?
I was also wondering if we could use this tool for structural variants where we only have data from one sample, or if there's a minimum number of samples recommended.