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?

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 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<http://www.ncbi.nlm.nih.gov/genome/assembly/2758/>
> with UCSC hg19 <http://genome.ucsc.edu> 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*
> *
>
>
> ___________________________________________________________
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> --
> Jennifer Jacksonhttp://galaxyproject.org
>
>
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