Hello Mathew,

Carlos is correct the the tools in the group "NGS: GATK Tools (beta)" will require that the data is mapped/associated with the reference genome "hg_g1k_v37". Belinda has offered to help with the details that go beyond Galaxy and that is great - the GATK forum is definitely the best resource for questions specific to that tools set once you know that the basic Galaxy datasets are correct.


Freebayes, on the other, will work with "hg19". Other users have perform an independent mapping run to avoid complex data manipulations/sorting.

Please feel free to send in a bug report if problems persist.

When submitted a bug report, send from the error dataset (just one is enough if all of the problems are in the same history) and put in the notes all of your concerns. Be sure to include this email address in the comments if your Galaxy account uses a different one. Also be sure to leave all input and error datasets that you would like feedback about in an undeleted state in your history. Undelete if necessary.

Thanks!

Jen
Galaxy team

On 8/6/12 7:30 AM, Mathew Bunj wrote:
I have been trying to use either Unified genotyper or Freebayes on one
of the Bam file. Both are failing.
1. With Unified genotyper it give me message saying Sequences are not
currently available for specified build. I have hg19 related data and
using default  settings  (pick up hg_g1k_v37 no other option). I am not
sure why it is giving me this error.
2. As an alternative I tried to run Freebayes with default setting and
choosing hg19 - it i snot giving any specific message but undetr bug
icon gives me -killed.
Now in order to make sure my Bam is OK, I tested out side Galaxy mPile
up and with in Galaxy pile up. Any suggestion why UNified genotyper is
not working. If needed I can share my history.
Thanks.


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___________________________________________________________
The Galaxy User list should be used for the discussion of
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