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 GRCh37http://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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