Sending to galaxy-dev ...

On Thu, Oct 27, 2011 at 5:51 AM, Jim Robinson
<jrobi...@broadinstitute.org> wrote:
>
> 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.

Useful background re: "Error reading bam file. This usually indicates
a problem with the index (bai) file. ArrayIndexOutofBoundsException:
4682 (4682)."

> The most common causes are (1) a problem with the sequence
> dictionary in the BAM header itself, specifically incorrect sequence
> lengths,

Any idea what tools produce that kind of thing?

> 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.

That is news to me - I recall "samtools index" being recommended
as a way to determine if a BAM files was sorted or not (error on
unsorted, you get an index if it was sorted) and again from
memory this is what Galaxy uses internally as part of preparing
BAM files on upload.

Might this be tied to a specific version of samtools? e.g. a
possible regression?

> 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

Thanks,

Peter

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