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 <s...@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.borr...@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 <s...@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 <j...@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: s...@unimelb.edu.au
>>> P: 03 903 53357
>>> M: 0414 854 759
>>> ___________________________________________________________
>>> The Galaxy User list should be used for the discussion of
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>>
>>
>
>
>
> --
> E: s...@unimelb.edu.au
> P: 03 903 53357
> M: 0414 854 759

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