Its possible the sorting problem was a specific version and now gives an error. The incorrect index caused by bad sequence lengths is a recurrent problem, but I do not know what tool produces such headers. Perhaps someone who has experienced this can chime in.

I'm not a samtools expert just sharing my experience on what has caused this error int the past. It does seem that, as a general rule, that these index problems result in errors from Picard (which the GATK uses), while samtools can fail silently and sometimes and give you an unrelated query region.

Jim

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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