Variable number of variants found over runs about mumandco

[SAMtoBAM]

Hi @elcortegano

I have oddly been able to reproduce the same problem on my end
Off the bat I have no idea what is causing this as there should not be any stochasticity...

I have traced the problem back to MUMmer...
If you look at the alignment files all produced by MUMmer using it's tools, specifically the 'test_query.delta_filter.coordsg' file
You will notice that the last alignment differs in position in the reference...
So any randomness comes from MUMmer

but the outcome is that the duplication is filtered out
Not sure I can do more than that unfortunately

[elcortegano]

To me it works for now knowing this. Thank you for the clarification!