Update: adaptation of a default run bam->pileup on my small test dataset gives 
the same result in my case using mpileup instead of pileup in the sam_pileup.py 
script (line 97).
Not tested any additional parameters though so there might be subtle 
differences in the outcome.

    #prepare basic pileup command
    cmd = 'samtools mpileup %s -f %s %s > %s'

Van: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: vrijdag 20 juli 2012 12:20
Aan: 'galaxy-dev@lists.bx.psu.edu'
Onderwerp: [galaxy-dev] samtools pileup deprecated

Hi All,

Maybe I missed it on the list here, but it seems that for samtools the pileup 
command has been deprecated without backward compatibility from the more recent 
samtools packages...

Did anyone rewrite some of the samtools tool wrappers for this....?
I am currently testing whether the Bam->pileup command can be easily changed in 
the sam_pileup.py script. But some functionality has gone and some additional 
is there. It seems I am up-to-date with the latest wrappers in the galaxy_dist 

Any pointers to recent wrappers would be welcomed.


Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to