If you feel it could be helpful, this is what I have so far as a
workflow for 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.
On Mon, Jan 23, 2012 at 7:44 AM, Clare Sloggett <sloc(a)unimelb.edu.au> wrote:
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.
On Thu, Jan 19, 2012 at 2:32 AM, Carlos Borroto
> 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,
> On Wed, Jan 18, 2012 at 12:00 AM, Clare Sloggett <sloc(a)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
>> - 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,
>> On Wed, Dec 7, 2011 at 4:24 AM, Jennifer Jackson <jen(a)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):
>>> If you are starting with a BAM file, convert BAM->SAM, then after
>>> back with SAM->BAM, using tools in the group "NGS: SAM Tools".
>>> Best regards,
>>> 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
>>>> 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.
>>> Jennifer Jackson
>> E: sloc(a)unimelb.edu.au
>> P: 03 903 53357
>> M: 0414 854 759
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