We have whole genome sequencing file aligned into a bam format file. Each sample has at least 2 bam files.
I want to find CNV Gain and Deletion from those bam files with Breakdancer, but I need to create a configuration file with bam2cfg.pl
They said I have to type : bam2cfg.pl -q [BDmapq] -n [readsToSample] bamfile > bd.config
How do I know BDmapq? How do I know readsToSample?
What's "bamfile" ? Is it the path to my bam file ? What's "bd.config" ??
Let's I have the following bam file /home/myfile.bam /home/myfile.bai
What do I do from here ??