Running Pindel individually per sample rather than running everything as it expects

Question

[mehmetgoktay1989]

Hi Everyone,

I would like to identify SVs including indels, deletions, tandem duplications and inversions.

I have tried to run samples first individually and then all of them at once. (lets say 3-4 samples).

It definitely gives different results for these two approaches.

Is there anyone who can tell me what is the reason? And what would happen if I run all samples individually and merge the output for futher processing.

(Does this approach decrease false positives?) - Because it outputs the way less SVs.

Thank you!