Hello all,

My users are trying to use a tool called bismark and it requires an unsorted 
SAM file for one of its steps

Previous steps produce BAM files so we would like to include the tool 
BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort 
by default and there is no way to alter this behaviour.

Is there another tool that would convert a BAM to a SAM without sorting it or 
can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result?



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