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