Hi Mike,

Are you using the Galaxy Main instance at http://usegalaxy.org? If not, can you duplicate when using Main?

If on Main, and you want to share a history link with me, I can take a look. Use "Options -> Share or Publish", generate link (or add me as a share user), and email that back to me directly.

Hopefully we can help,

Jen
Galaxy team

On 10/26/11 9:34 PM, Mike Dufault wrote:
Hello Galaxy Team,
I have been using Galaxy for SNP detection for with great success.
Basically, I followed the screen-cast from Anton without any problems.
The only change was to use the BWA instead of Bowtie. Until now, I have
always assigned my raw read files to the hg19 format. Now I want to try
the GATK pipeline to analyze my samples but I am running into a problem
with the bam/bai files.
Here is what I did. I imported my Illumina paired end reads into Galaxy
and assigned them to the hg_g1k_v37 format instead of the Hg19 format.
 From there, I again followed the exact same process: FastQ Groomer,
Summary Statistics, Boxplots, Align with BWA, filter on SAM, SAM-to-Bam,
generate bai file. I made sure that hg_g1k_37 was chosen for the format
for all of these steps that required that information.
Everything seemed to run successfully as all of the boxed turned green.
When I tried to view the bam file in IGV (as a QC step before the GATK
pipeline), I received the following error: "Error reading bam file. This
usually indicates a problem with the index (bai) file.
ArrayIndexOutofBoundsException: 4682 (4682)."
I did the exact same analysis using the Hg19 format and my bam/bai files
worked perfectly fine in the IGV viewer. Can anyone tell me what the
problem is and how to fix it?
Thanks,
Mike Dufault



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___________________________________________________________
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
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use the Galaxy Development list:

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