Hi Mike,
Someone from the Galaxy team can perhaps give some insight on what went
wrong, I can comment on the error message from IGV. That error is
thrown from Picard, in every case I've investigated so far it was traced
to a problem with the index. The most common causes are (1) a problem
with the sequence dictionary in the BAM header itself, specifically
incorrect sequence lengths, and (2) indexing an un-sorted BAM.
Apparently samtools will make invalid indexes from such files without
any complaints in both cases. You can even use samtools tview on such
files, it happily will show you some random region when you query.
I don't see a "Sort" step in your workflow, maybe that's the problem?
Please CC me on any reply, I might miss it in the list.
Jim
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
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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