Hello Ryan,

I'm in the exact same situation with my bowtie/tophat tools,
going back and forth between outputing a SAM, sorted SAM, BAM or sorted BAM,
and I'm still not sure what's the best method.

Storage wise - you're correct, just saving the sorted BAM is the best (even 
more with the fact the processing SAM files as text is so horrendous that I 
think alnost no tool uses them directly, always requiring intervals or sorted 

But one annoyance (for me) is that samtools (the program) is very in-efficient 
- using only a single thread (and the sort part isn't doing a great job at 

So if I give the "mapping" tool as a whole 20 threads or more, and a part of 
the running time (the samtools sort part) is only using a single-thread - I'm 
wasting the other threads, as they sit idle waiting for the sort to finish.

I also tried sorting the SAM file directly, using GNU sort (version 8.10 can 
use multiple threads, and the memory management actually works, as opposed to 
"samtools sort -m") - but I'm not sure it's worth the effort.

I didn't find an optimal solution that I like, and I'm interested to hear what 
others think.


Ryan Golhar wrote, On 04/05/2011 01:08 PM:
> 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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