[galaxy-user] Problem with bam and/or bai files

[Jennifer Jackson]

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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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support