I have a family of 5 samples. 2 are affected by a disease and 3 unaffected. I want to do a CNV analysis using the tool BreakDancer. I am a little confused as to how I should generate the config file, should I give all the 5 bam files as an input to bam2Config.pl? or should I make two separate config files for the affected and unaffected groups?
Any help is much appreciated. Thank you!