I have a doubt while running the cnv-seq.pl script. Currently am working on rice genome to identify the copy number variants. Two files are required to run the above script . I got test.hits file by aligning the reference genome with test genome using samtools which is mentioned in the tutorial. In the cnv-seq tutorial they said ref.hits. But they did not mention how to generate this file.
I am very much confused because i already aligned my test genome with reference genome and got map locations.