I'm using a couple programs to look at repetitive DNA in mapped reads (bamfiles): genotan and repeatseq. Both programs have publications and are designed to work on bamfiles.
The problem is that I'm getting segmentation faults from both programs on some of the bamfiles I would like to analyze. It's hard to tell for sure why some bamfiles run successfully while others seg fault. There does appear to be a much greater tendency to seg fault on any bamfile created with bwa. Im wondering if there are any formatting differences between bwa and bowtie2 mapped bamfiles and if there is a way to repair the files that fail without remapping. Perhaps its a whitespace issue or special character issue. Debugging the programs myself is probably unfeasible so Im looking for any other solution, Thanks