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?


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