final bam files

[mikebaravo]

Hi all,

I just started switched from my selfmade in-house basic pipeline to SeqMule.
I was wondering what the final bam file is.
I assume that the .0.0_bwamem.sort.rmdup.readfiltered.bam
and .0.0_bwamem.sort.rmdup.bam etc. are temporary but what about
_bwamem.merge.realn.bam and ID_bwamem.merge.realn.bam.
The 38490-MS_bwamem.merge.realn.bam is the last one that is generated so i used this for further downstream extracts.
I hope I chose the right one.
To overcome this and to save some hdd space, is there a way to do some clean up and delete them besides having a clean up script?

Thanks a lot!
BW,
MB