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' try: Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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... http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html 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 repository. Any pointers to recent wrappers would be welcomed. Alex