Which option do you use with Breakdancer ? I usually write no options like that
perl bam2cfg.pl input.bam > input.cfg breakdancer input.cfg > output.txt
I saw that some experts use the -g and -h options, I've read the readmefile and I still don't understand what difference does it make..
If you want to have CNV Gain AND Loss from paired-end sequencing which option would you use ?
ps : I'm a breakdancer newbee (>.<)