Hi Clare,

I ran into a similar question testing out GATK pipeline on Galaxy. My solution was to always convert my SAM files to BAM. The wrapper also sorts the final BAM file output and it does this using the known 'samtools sort', which sorts chromosomes in the same order of the reference genome. The reference genome can be automatically selected by the build associated with the dataset or choose from the history.

I haven't confirmed if a conversion from BAM to SAM would do the same thing.

Hope it helps, Carlos

On Wed, Jan 18, 2012 at 12:00 AM, Clare Sloggett sloc@unimelb.edu.au wrote:

Hi Jen,

Thanks for this, belatedly!  And happy new year!

I think this will work for some of my cases but possibly not all, since it looks like chromosomes are being sorted alphabetically. It depends what the reference genome used was and what tools you're planning to use after sorting as to whether this is ok.

I was initially just wondering why 'samtools sort' hadn't been wrapped

• not as a complaint, but since the various other samtools options

mostly seem to be already wrapped, I wondered if there was some particular reason not to have this one. If I were to try to wrap 'samtools sort' myself is there some difficulty I should know about?

Thanks again, Clare

On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson jen@bx.psu.edu wrote:

...

Hello Clare,

An example of how to sort a SAM file is included in the workflow from #2 on this FAQ (it can be imported and the sort modified as needed): http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq

If you are starting with a BAM file, convert BAM->SAM, then after sorting, back with SAM->BAM, using tools in the group "NGS: SAM Tools".

Best regards,

Jen Galaxy team

On 12/4/11 9:45 PM, Clare Sloggett wrote:

...

Hi galaxy users,

Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy?

I think this has probably been discussed before, sorry. I just want to check I haven't missed anything, since sibling tools from e.g. the samtools and picard suites are wrapped.

Thanks, Clare

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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Hi Claire,

Your welcome!.

If you feel it could be helpful, this is what I have so far as a workflow for GATK: http://test.g2.bx.psu.edu/u/cjav/w/gatk

Is not complete, but I think it could be a good starting point. Please if you ended using this workflow as a starting point and find something you think it could be improve, let me know. There are things like which annotations or ROD file I should use, that I haven't been able to quite understand.

Regards, Carlos

On Mon, Jan 23, 2012 at 7:44 AM, Clare Sloggett sloc@unimelb.edu.au wrote:

Hi Carlos,

Thanks! I didn't realise the conversion was doing that.

In fact I want bam files (I'm also using GATK) so this is really helpful.

Cheers, Clare

On Thu, Jan 19, 2012 at 2:32 AM, Carlos Borroto carlos.borroto@gmail.com wrote:

...

Hi Clare,

I ran into a similar question testing out GATK pipeline on Galaxy. My solution was to always convert my SAM files to BAM. The wrapper also sorts the final BAM file output and it does this using the known 'samtools sort', which sorts chromosomes in the same order of the reference genome. The reference genome can be automatically selected by the build associated with the dataset or choose from the history.

I haven't confirmed if a conversion from BAM to SAM would do the same thing.

Hope it helps, Carlos

On Wed, Jan 18, 2012 at 12:00 AM, Clare Sloggett sloc@unimelb.edu.au wrote:

...

Hi Jen,

Thanks for this, belatedly!  And happy new year!

I think this will work for some of my cases but possibly not all, since it looks like chromosomes are being sorted alphabetically. It depends what the reference genome used was and what tools you're planning to use after sorting as to whether this is ok.

I was initially just wondering why 'samtools sort' hadn't been wrapped

• not as a complaint, but since the various other samtools options

mostly seem to be already wrapped, I wondered if there was some particular reason not to have this one. If I were to try to wrap 'samtools sort' myself is there some difficulty I should know about?

Thanks again, Clare

On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson jen@bx.psu.edu wrote:

...

Hello Clare,

An example of how to sort a SAM file is included in the workflow from #2 on this FAQ (it can be imported and the sort modified as needed): http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq

If you are starting with a BAM file, convert BAM->SAM, then after sorting, back with SAM->BAM, using tools in the group "NGS: SAM Tools".

Best regards,

Jen Galaxy team

On 12/4/11 9:45 PM, Clare Sloggett wrote:

...

Hi galaxy users,

Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy?

I think this has probably been discussed before, sorry. I just want to check I haven't missed anything, since sibling tools from e.g. the samtools and picard suites are wrapped.

Thanks, Clare

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759