Hi Rich,

You could do this or you could switch to this version of the human genome (is in all of Galaxy's tools, but will not be useable at UCSC):

Human (Homo sapiens) (b37): hg_g1k_v37


Galaxy team

On 6/6/12 7:30 AM, Richard Linchangco wrote:
Dear Jen,

Thanks again!

Does this mean I should upload a "Custom Reference Genome"?
I have downloaded the genome specified by GATK for hg19. All I must do
is upload to ftp, map it again, and then it should let me use it later
on for "Counting Covariates" and the such?


On Wed, Jun 6, 2012 at 9:55 AM, Jennifer Jackson<j...@bx.psu.edu>  wrote:
Hi Rich,

Additional genomes will be specially sorted, indexed, and added to the GATK
tool suite as it moves out of beta status. Hg19 is short-listed for addition
near term.

We do take requests to have genome added to tools and consider these when
ranking our prioritization lists. Which genome did you want to use?

One small warning when using a custom reference genome with this particular
tool set - be sure to visit the GATK web site links directly to understand
the sorting criteria for genomes. It can be different than how Galaxy, UCSC,
and many of the existing tools already sort or instruct users to sort
genomes or data. In short, the genome must be sorted in the exact order that
it was originally released, but even this can be slightly confusing,
especially if working with a non-human genome as there are few examples.
Still, the documentation can help and tools are easily tested (if the
sorting is wrong, the tool will fail and let you know).

If others have requests for GATK native genomes, they are also welcome to
reply. In general, key model organisms would be ranked highest in priority.
We also try to get the largest genomes loaded natively first (for purely
practical reasons).

Good question, thanks!

Galaxy team

On 6/5/12 8:01 AM, Richard Linchangco wrote:

Dear Galaxy,

I've been searching the lists for this type of issue and only found
one solution thus far which is the use of a custom reference. It
doesn't make sense in my situation because the reference I used was
from Galaxy itself when I mapped my data. I'm now trying to use GATK
to find SNPs but no matter what I've tried I can't get past this
issue. I'm trying to use the Count Covariates and the Unified
Genotyper but to no avail. The only issue appears to be that
"Sequences are not currently available for the specified build."

Any help would be much appreciated. Thanks


Jennifer Jackson

Jennifer Jackson
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