9 Feb
2012
9 Feb
'12
3:57 a.m.
On Thu, Feb 9, 2012 at 2:57 AM, Fields, Christopher J <cjfields@illinois.edu> wrote:
Forgot to add, but this also seems tied to the same problem Ryan's describing. IIRC Galaxy also runs 'samtools sort' after certain jobs, correct?
chris
This sounds like part of the "BAM grooming" (assuming that's what the Galaxy team call it, based on their term "FASTQ grooming") which tries to ensure BAM files are coordinate sorted and indexed on upload/import etc. Perhaps this is a general symptom of file format conversion also being done on the server rather than as a cluster job? Peter