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 ?