Hi Mathew,

If you are new to the GATK tools you may want to read some of our introductory materials at this link:
http://www.broadinstitute.org/gatk/guide/topic?name=intro

You will find some documents explaining what input files you can use, what are the constraints, and plenty of information about using tools like the Unified Genotyper in the GATK Guide. 

If you have questions that are specific to the GATK tools, feel free to ask them in our forum and we will do our best to help you.
http://gatk.vanillaforums.com/

Good luck!



On Tue, Aug 7, 2012 at 2:01 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
Hi Mathew,

Regarding 1 you might want to read this thread:
http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html

All tools from GATK are limited to hg_g1k_v37 as far as I know.

Best,
Carlos

On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj <mathewbunj@yahoo.com> 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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___________________________________________________________
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