Pindel : Differences between results from using bam2pindel then pindel and only pindel

Question

[FryHandiz]

Hello everybody,

I used bam2pindel (b2p) with pindel then only pindel without b2P and I don't obtain the same result. Indeed, I have write a script which can detect the differences and it turns out that certain SV are found and others aren't if we use pindel only or with bam2pindel, do you know why? Thank you.