On Thu, Jun 21, 2012 at 10:50 AM, Lilach Friedman <lilachfr@gmail.com> wrote:
> Hi Jennifer,
> Thank you for this reply.
>
> I made a new BWA file, this time using the hg19(full) genome.
> However, when I am trying to use DepthOfCoverage, the reference genomr is
> stucked on the hg_g1k_v37 (this is the only option to select), and I cannot
> change it to hg19(full). Most probably, because I selected hg_g1k_v37 in the
> previous time I tried to use DepthOfCoverage.
> It seems as a bug? How can I change it?
>

Hi Lilach,

I have been dealing with these issues for some time now.

The only genome you can use with Picard and GATK tools in Galaxy is
hg_g1k_v37. I think this is why.

>From GATK Wiki[1]:
"If you are using human data, your reads must be aligned to one of the
official b3x (e.g. b36, b37) or hg1x (e.g. hg18, hg19) references. The
contig ordering in the reference you used must exactly match that of
one of the official references canonical orderings. These are defined
by historical karotyping of largest to smallest chromosomes, followed
by the X, Y, and MT. The order is thus 1, 2, 3, ..., 10, 11, 12, ...
20, 21, 22, X, Y, MT. The GATK will detect misordered contigs (for
example, lexicographically sorted) and throw an error. This draconian
approach, though unnecessary technically, ensures that all
supplementary data provided with the GATK works correctly. You can use
ReorderSam to fix a BAM file aligned to a missorted reference
sequence."

[1]http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK

So far what I have done when presented with a BAM file produced with
reference with lexicographical chromosomes ordering, is to use
Picard's ReorderSam tool, also in Galaxy, selecting hg_g1k_v37 as
reference. You might not be able to this, as if a recall correctly
hg19 also use chr1, chr2... instead of 1, 2, ... In that case more
work needs to be done and at that point is almost easier to just remap
with the correct reference for use with GATK. In your case it seems
you already have it. What you might need to do is resort your
intervals file and probably change the chromosomes identifiers, this I
think can be done inside Galaxy.

I would love to hear comments about this approach, as sometime I do
worry like Hiram's comment hints to, that hg19 and hg_g1k_v37 might
not be completely identical beside the chromosome ordering. In that
case my resorted BAM or intervals files might be incorrect.

Hope it helps,
Carlos

> Thanks,
>   Lilach
>
>
>
> 2012/6/18 Jennifer Jackson <jen@bx.psu.edu>
>>
>> Hi Lilach,
>>
>> The problem with this analysis probably has to do with a mismatch between
>> the genomes: the intervals obtained from UCSC (hg19) and the BAM from your
>> BWA (hg_g1k_v37) run.
>>
>> UCSC does not contain the genome 'hg_g1k_v37' - the genome available from
>> UCSC is 'hg19'.
>>
>> Even though these are technically the same human release, on a practical
>> level, they have a different arrangement for some of the chromosomes. You
>> can compare NBCI GRCh37  with UCSC hg19 for an explanation. Reference
>> genomes must be exact in order to be used with tools - base for base. When
>> they are exact, the identifier will be exact between Galaxy and the source
>> (UCSC, Ensembl) or the full Build name will provide enough information to
>> make a connection to NCBI or other.
>>
>> Sometimes genomes are similar enough that a dataset sourced from one can
>> be used with another, if the database attribute is changed and the data from
>> the regions that differ is removed. This may be possible in your case, only
>> trying will let you know how difficult it actually is with your analysis.
>> The GATK pipeline is very sensitive to exact inputs. You will need to be
>> careful with genome database assignments, etc. Following the links on the
>> tool forms to the GATK help pages can provide some more detail about
>> expected inputs, if this is something that you are going to try.
>>
>> Good luck with the re-run!
>>
>> Jen
>> Galaxy team
>>
>>
>> On 6/18/12 4:42 AM, Lilach Friedman wrote:
>>
>> Hi,
>> I am trying to used Depth of Coverage to see the coverages is specific
>> intervals.
>> The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy
>> and the file type was changed to intervals.
>>
>> I gave to Depth of Coverage two BAM files (resulted from BWA, selection of
>> only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM)
>> and the intervals file (in advanced GATK options).
>> The consensus genome is hg_g1k_v37.
>>
>> I got the following error message:
>>
>> An error occurred running this job: Picked up _JAVA_OPTIONS:
>> -Djava.io.tmpdir=/space/g2main
>> ##### ERROR
>> ------------------------------------------------------------------------------------------
>> ##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0):
>> ##### ERROR The invalid argume
>>
>>
>> Is it a bug, or did I do anything wrong?
>>
>> I will be grateful for any help.
>>
>> Thanks!
>>    Lilach
>>
>>
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
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>> --
>> Jennifer Jackson
>> http://galaxyproject.org
>
>
> ___________________________________________________________
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