How do I compare reads between two bam file?
I would like to find reads in one bam files which are not in a second bam file.
Is there an easy way to do this?
My way for now is:
- sort both bam files by read name
- extract read headers of both files (using
cut -f1
) for easier handling - run
diff
on both files - manually search for differences
But this seems to me very tedious. Is there a better way?
thanks
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