Converting VCF to gd_genotype

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Converting VCF to gd_genotype

Mike Montague
I'm interested in using the Genomic Diversity tools. I've used these
with success for a previous project. For this current project, I've
converted a vcf file (29 subjects) to a gd_genotype file. When I attempt
to specify individuals, the checkboxes for each subject are not present.
Without specifying individuals, I am unable to complete other analyses
(overall FST, etc.)

I cannot distinguish a difference between the vcf files that were
successful from the previous project and this current project's vcf, but
I assume there is a format difference that I cannot detect.

I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21
22:09:49 2014 (UTC). I can share the histories of the projects if necessary.

Mike

--
____________

Michael J. Montague, Ph.D.
Post-Doctoral Research Associate
The Genome Institute, Washington University School of Medicine
4444 Forest Park Avenue, Campus Box 8501
St. Louis, MO 63108
T. 718.809.4093


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Re: Converting VCF to gd_genotype

Jen Hillman-Jackson
Hello Mike,

Yes, we have similar recent reports of issues with tools from this group
and are actively investigating the root cause. It is unknown whether or
not python version is related, but right now we are tracking the issues
under a single ticket with that as a suspected contributing factor. You
can follow this ticket, and any tickets that branch from it, here:
https://trello.com/c/yXrDICmg

Our apologies for the current inconvenience,

Jen
Galaxy team

On 2/23/14 2:40 PM, Mike Montague wrote:

> I'm interested in using the Genomic Diversity tools. I've used these
> with success for a previous project. For this current project, I've
> converted a vcf file (29 subjects) to a gd_genotype file. When I
> attempt to specify individuals, the checkboxes for each subject are
> not present. Without specifying individuals, I am unable to complete
> other analyses (overall FST, etc.)
>
> I cannot distinguish a difference between the vcf files that were
> successful from the previous project and this current project's vcf,
> but I assume there is a format difference that I cannot detect.
>
> I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21
> 22:09:49 2014 (UTC). I can share the histories of the projects if
> necessary.
>
> Mike
>

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org