Do you mean a SAM/BAM file sorted by read name?
If so, try samtools sort -n ... instead.

Peter

On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott
<alistair.chilc...@utas.edu.au> wrote:
> 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?
>
>
> Regards,
>
> Alistair
>
>
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