Bam2Cfg.Pl And Breakdancer

Question

[madkitty]

We have a whole genome sequence data on BAM file and want to detect INTER AND INTRA chromosomal rearrangement. I need to create a config file to use with breakdancer. The config files are create with bam2cfg.pl.

• PROBLEM #1

This bam2cfg.pl. software has a lot of options and I'm not familiar with it. If I do the following command :

 perl  bam2cfg.pl. myfile.bam > myconfigfile.cfg   #This works well

 perl bam2cfg.pl. -g -h myfile.bam > myconfigfile.cfg     #This doesn't work and returns..

 Use of uninitialized value in printf at bam2cfg.pl line 222.

• PROBLEM #2

We want to identify CNV Loss and Gain with Breakdancer, but when I look at the pipeline it only gives an example for inter-chromosomal rearrangerement. Which options should I use with bam2cfg.pl. and breakdancer to have CNV Loss and Gain ?

[Chirag Nepal]

Would you please share your experience on how you ended up (the parameters) using breakdancer.