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total time 0.06
From: Daniel Blankenberg [d...@bx.psu.edu]
Sent: Wednesday, December 12, 2012 4:29 PM
To: Farooq,Umar (res)
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] GATK Not running
Hi Umar,
Can you click the eye icon to view the contents
Hi Umar,
Can you click the eye icon to view the contents of the 'log' dataset for the
GATK run. The end of the log should have the actual error encountered (the text
you provided is a bit of a red herring)
Since you are using hg19, the most likely cause for the error is that the
reference
Hi Philippe,
The GATK wrappers provided with the Galaxy distribution are for GATK version
1.4. There is a set of 1.6/GATK-lite wrappers that has been developed by the
team, but is not yet available. There may also be other options available in
the Tool Shed that have been contributed by the
Hi Joshua,
Is this on the main public site? If so, can you share your history with me and
I'll take a look? If this is on a local instance, can you provide additional
information, such as the GATK version that you are using?
Thanks for using Galaxy,
Dan
On Dec 11, 2012, at 5:34 PM, Joshua
Hi,
I am trying to incorporate GATK in my pipeline but not been able to make it
work. I aligned my data with Hg 19 and then ran sam tool filter and then picard
duplicate removal. I uploaded dbSNP and the reference FASTA file for Hg 19 in
galaxy to run this pipeline. But for some reason GATK
Hi,
I have encountered the same kind of errors. When I update the loc files
link to GATK, some of the tools display the reference genomes I added and
some not. It seems that the galaxy wrapper for GATK 1.6 is not very
functional. GATK don't really care because they are not supporting it any
more,
I'm having some problems with GATK as well, but do have a functional
pipeline that uses the following GATK tools in Galaxy:
- Realigner Target Creator
- Indel Realigner
- Unified Genotyper
- Variant Filtration
The main problem I'm having with them is that it seems I need to run the
fasta/fastq
cannot use GATK in galaxy.
From: Joshua Orvis [jor...@gmail.com]
Sent: Tuesday, December 11, 2012 5:34 PM
To: Philipe Moncuquet
Cc: Farooq,Umar (res); galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] GATK Not running
I'm having some problems
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