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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