cmuschwartzlab/mosaicsim

mosaicsim's Issues

questions about paired exon sequencing

Hi,
I have a few questions regarding the exonrunPairedSim function and wonder if you could provide some insights.

1. The coverage was achieved when cov exceeds coverage using cov += 2batchsubblockratio where ratio = 2rl/fl. Can you briefly explain why it is necessary for the multiplication of 2 at both positions?
2. It seems to me that you are adding all the mutations for a tumor clone and creating a .gz file first then do the sampling on the exon regions using the provided file. How do you handle the fragments/reads for positions/regions where there is CNV or DEL before the position?
3. The coverage can be achieved by repeated sequencing for the exon regions. Does it mean each exon region will have similar coverage even if there is CNV or DEL events? i.e. will the generated reads differ in coverage such that copy number calling tools can be used to infer CNV using exon sequencing data?
   Thank you in advance for helping with the questions!