Dear all, 

during a step of a CNV analysis on cancer genomes, I would like to be able to COUNT and DISPLAY along the CHROMOSOME AXIS the NUMBER of READS in 10KB REGIONS of GERMLINE and CANCER GENOMES. 

I would like to ask you please for your suggestions about : 

-- any fast function/algorithm that COUNTS the reads from a BAM file in 10kb windows ?

-- a package/function that DISPLAY the COUNTS along the chromosome axes ? 

many thanks, 

bogdan
 
You should be able to do it with `bedtools`. First generate a BED file of 10kb regions with `bedtools makewindows`. Then calculate coverage for those regions with `bedtools coverage`.

Alternatively, you can try `deepTools bamCoverage` to generate a coverage track (you can specify the size of bins).

Of course, whatever package you are using for CNV calling should have an option to generate some sort of graphical output.