using Breakdancer for mate pair

[ilovekk1989]

Dear all ,

I have a little problem about BreakDancer.

I have a mate-pair data from Illumina , and I use some tools to reverse and trim each read.

now I want to use Breakdancer to find discordant reads ,

and I use this command :

perl BreakDancerMax.pl -l -f -o Chr6 5k.sorted.config > 5k_sorted.l.chr6.max

I want to know should I use option "-l" .

Because if I use it , breakdancer will find so many insertions and their size are about 3500.

If I wont use -l , breakdancer still find structural variations but total is lower than I use -l .

thank you guys.