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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