Hello all,
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 different, 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 updated package than changes the results?
By the way the first analysis was made one year ago with the 0.7 version.
I looks like you're not using the same filtering criteria as in the original study. From the manual:
How do you set these parameters values? Do you use the same ones as in the original study?
Yes exactly the same because I copied the BAM files and the config files that SVDetect needs.