detecting CNVs from low-pass whole genome shotgun data

The program requires 3 input files:

  1. Reference fasta file
  2. Mapview file - alignment from MAQ by Heng Li.
  3. Parameter file with genome type, prior estimated number of CNVs, average CNV size, depth coverage, and read size

Running the program
After compiling all the .java files, use command in the following format:
java Main -r reference.fasta -m mapview -p parameters