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 repository.

 

Any pointers to recent wrappers would be welcomed.

 

Alex