How do I compare reads between two bam file?

How do I compare reads between two bam file?

1

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:

  1. sort both bam files by read name
  2. extract read headers of both files (using cut -f1) for easier handling
  3. run diff on both files
  4. manually search for differences

But this seems to me very tedious. Is there a better way?

thanks


samtools


reads


bam


compare

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