Hi, I wonder if it is possible to get different resulting alignments using the same reads and the same reference as input?
I did the alignment step twice and my BAM-files from the two runs differ slightly. I used BWA for the alignment step.
Is there any possibility that BWA's decisions where to align a read can differ within two runs having exactly the same parameters and input?
Are there any "random" steps in the algorithm? Does multi-threading affect the alignment?
Furthermore I found, that the regions differing in between the two BAMs showed strikingly low read-quality. But I don't know if this has something to do with the observed problem.
Any help or further insight is appreciated.