[galaxy-dev] Optimizing Disk space using by combining mapping with SAM-to-BAM

[Ryan Golhar]

Hi all - I find it redundant to hold on to SAM output from NGS Mapping 
tools such when I end up converting the SAM files to BAM files anyway. 
The cleanup scripts require the history items to be deleted, but I don't 
want to delete them yet as I want the entire workflow to be kept until 
we are done analyzing our data.

So, I was thinking of a way to remove the intermediate SAM files and 
thought how I would do this on the command line...simply pipe the output 
of BWA to samtools to create a BAM file and never have a SAM file to 
deal with.

The BWA tool runner can be modified to pipe BWA output directly to 
samtools so a SAM file is never physical stored on disk.  Has anyone 
done this?  Does this seem like a good idea?

Ryan

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