I'm using SVDetect in order to do an analysis which was already done in my company (I just wanted to try this soft), I started with the same BAM files, and the same config files, and finally I found around 9,000 SV whereas the first analysis found 50 SV. Of course the person who did that is not in my company anymore :D.
I've tried SVDetect 0.7 and 0.8 as well, at each time I found around 9,000 SV (not exactly the same number).
Using diff command I can say *.bam *ab.bam and *am.bam.links are the same in both analysis. But *ab.bam.links.filtered.sv.txt are differents, indeed it contains more than 20,000 lines in my analysis against only 120 in the other one... So the difference arrives at the "filtering" step.
I don't understand what's going on, do you guys thinks it could be an upadated package than changes the results ?
By the way the first analysis was made one year ago with the 0.7 version.