what files are produced from CNVnator ?

[Kennels]

Hi,

I'm wondering if anyone can let me know what outputs to expect from CNVnator for each step.
I've followed the instructions in the readme file, and except for the last step (-view), calculations appear to proceed without any errors. Only 1 file is being created and updated - the .root file. Are there supposed to be any other directories or files?

When i run the last command (-view), it says it can't find the 'bin' directories or the read depth histogram. These are indeed not in the working directory.

I've asked the author but didn't get any reply.

background: it might be that my inputs are not correct. I'm trying to run this on a .bam file from an alignment of 100 PE reads to a 12kb scaffold/reference. A total of 4291024 reads were placed.

Thanks,

[dmacmillan]

If you generate a histogram you are asked to input the bin size, therefore you will only be able to view a histogram of that particular size. I believe you must also go through signal partitioning before viewing.