I have a question regarding a warning that I am observing while merging bam files with samtools.
For simplicity here is the command I used for a single pair of files:
samtools merge merged.bam File1-sorted.bam File2-sorted.bam
Note that I simply added the 'sorted' on input files just to clarify that these files were previously sorted with samtools.
After running 'merge', the following warning is issued:
'Order of targets in file File2.bam caused coordinate sort to be lost'
Unfortunately, I am having a hard time finding more details about what this means, and how to avoid. I would appreciate any information. Thanks!