I need to do a complement between two bam files. I have tried to use the diff function in bamUtils to find the differences between the two, but when I'm trying to use samtools to run further analyses it is telling me that I have a truncated file. I haven't been able to find out if bamUtils is using a different end of file character than samtools is looking for or not. That is the only reason that I can think of as to why it would come up with a truncated file and not find the EOF character. Is there a way to do a complement between two bam files with samtools or possibly picard? I have not been able to find any sites online where they have said if they can or not.