[galaxy-user] Sort & index SAM-files automatically

Hello!

I convert SOLiD csfasta- and qual-files to fastq-files and map those against Hg19 (Bowtie).

I would like to use the resulting sam-files in the IGV browser (Broad Institute).

Therefore, the sam-file need to be sorted an indexed. This could be done using the “igvtools”.

However, it would be nicer if this sorting and indexing could be done automatically using GALAXY.

I guess that it is certainly possible – but I do not know how.

Could anybody let me know how it works and what function I have to use, respectively?

How can I sort the sam-file the correct way?

Thank you in advance.

Best regards

Jo