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
 
Have a look at [indexcov][1], but its intervals are of 16kb.


  [1]: https://github.com/brentp/goleft/tree/master/indexcov