From Genome Analysis Wiki
--in2 : second coordinate sorted SAM/BAM file to be diffed
--seq : diff the sequence bases.
--baseQual : diff the base qualities.
=== Output Format ===
There are 2 types of differences.
* ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff
If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3.
==== Example Output ====
../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log
> cd *:0 * * *
== readReference ==