Hi all, I appreciate all of the discussion related to this issue. I still don't understand why I should only see this issue when I choose the hg_g1k_v37 format but not when I choose the Hg_19 format? I realize that I would need to ensure that the Bam files are sorted correctly before I enter the GATK pipline, but all of this is before that process. When my read files are processed through to .bam files using the hg_19 format, I can view them in IGV without a problem. It is only when I use the hg_g1k_v37 format that I receive an error from IGV. It seems to me that the process that I am using in Galaxy should be identical except for the reference genome format (i.e. hg_19 or hg_g1k_v37). I am at a loss of how to proceed. Does anyone have ideas? Thanks, Mike
--- On Thu, 10/27/11, Jim Robinson <jrobi...@broadinstitute.org> wrote: From: Jim Robinson <jrobi...@broadinstitute.org> Subject: Re: [galaxy-user] Problem with bam and/or bai files To: "Peter Cock" <p.j.a.c...@googlemail.com> Cc: "Galaxy Dev" <galaxy-...@bx.psu.edu>, "Mike Dufault" <dufau...@yahoo.com>, "galaxy-user" <galaxy-u...@lists.bx.psu.edu> Date: Thursday, October 27, 2011, 9:58 AM 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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