I've been looking through all the Breakdancer docs for more detailed description of the options in bam2cfg.pl - specifically for what -s represents. The 'minimal mean insert size' seems a little ambiguous. If it was 'minimum insert size' or 'mean insert size' I'd know exactly what it means, but 'minimal insert size' doesn't make any sense yet it seems that it likely needs to be modified from the default value for large insert libraries. Not sure how critical this is but the documentation for the bam2cfg is very limited. Thanks for any help/clarification.
I'm looking through the code here and it seems as though for each library in your bam file, bam2cfg says "what's the mean insert size of this library?". Then it checks to see if that mean insert size is below the minimum threshold, (set with -s). If so, it skips that library. So really, it is properly named, although I understand your confusion.
I also have a question on Bam2Cfg Parameter Description. What is the difference between minimum mapping quality and alternative mapping quality? If lets say I'd like to use minimum mapping quality 30, do I need to include -m ( Using mapping quality instead of alternative mapping quality) or -q (Minumum mapping quality ) or both?
perl bam2cfg.pl -m -q 30 bam_file ?
It's very confusing because if say I use minimum mapping quality, for BreakDancerMax on the other hand there is -q parameter ( minimum alternative mapping quality ). And there is no parameter for minimum mapping quality like bam2cfg.pl. However in the explanation of the parameters, it stated -q is minimum mapping quality, not alternative mapping quality.
-q INT minimum alternative mapping quality 
"The -q specifies the MAQ mapping quality threshold and can be used to skip reads that are not confidently mapped."
Hopefully someone can help me shed some light on this.