Hello Lilach,

Currently, the human reference genome indexed for the GATK-beta tools is 'hg_g1k_v37'. The GATK-beta tools are under active revision by our team, so we expect there to be little to no change to the beta version on the main public instance until this is completed.


Attempting to convert data between different builds is not recommended. These tools are very sensitive to exact inputs, which extends to naming conventions, etc. The best practice path is to start and continue an analysis project with the same exact genome build throughout.

If you want to use the hg19 indexes provided by the GATK project, a cloud instance is the current option (using a hg19 genome as a 'custom genome' will exceed the processing limits available on the public Galaxy instance). Following the links on the GATK tools can provide more information about sources, including links on the GATK web site which will note the exact contents of the both of these genome versions, downloads, and other resources.

Hopefully this helps to clear up any confusion,

Best,

Jen
Galaxy team

On 6/21/12 7:50 AM, Lilach Friedman 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?

Thanks,
  Lilach


2012/6/18 Jennifer Jackson <j...@bx.psu.edu <mailto: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 Jackson
http://galaxyproject.org



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