Thank you very much for this explanation.
The format of my intervals file is:
Can you please explain me how to change this format so I will be able to
give it as an input to DepthOfCoverage
2012/6/21 Carlos Borroto <carlos.borr...@gmail.com>
> On Thu, Jun 21, 2012 at 10:50 AM, Lilach Friedman <lilac...@gmail.com>
> > 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
> > change it to hg19(full). Most probably, because I selected hg_g1k_v37 in
> > 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:
> "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
> 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,
> > Thanks,
> > Lilach
> > 2012/6/18 Jennifer Jackson <j...@bx.psu.edu>
> >> Hi Lilach,
> >> The problem with this analysis probably has to do with a mismatch
> >> the genomes: the intervals obtained from UCSC (hg19) and the BAM from
> >> BWA (hg_g1k_v37) run.
> >> UCSC does not contain the genome 'hg_g1k_v37' - the genome available
> >> 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.
> >> 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.
> >> they are exact, the identifier will be exact between Galaxy and the
> >> (UCSC, Ensembl) or the full Build name will provide enough information
> >> 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
> >> the regions that differ is removed. This may be possible in your case,
> >> trying will let you know how difficult it actually is with your
> >> The GATK pipeline is very sensitive to exact inputs. You will need to be
> >> careful with genome database assignments, etc. Following the links on
> >> 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
> >> 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
> > ___________________________________________________________
> > The Galaxy User list should be used for the discussion of
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The Galaxy User list should be used for the discussion of
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