Re: [Samtools-help] error in IGV due to Picard or indexing bam through samtools

[Alec W. <al...@br...>]

Hi Pawel,

Your BAM index may not be valid.  Try rebuilding it.

-Alec


On Fri, Apr 26, 2013 at 2:39 AM, Pawel Osipowski
<paw...@gm...>wrote:

> Hi,
> Could somebody help me with this?
>
> The error occurs in IGV and comes from "Picard", as I was instructed by
> IGV staff.  The problem recurs after regenerating  an index. The relevant
> portion of the log is below.
>
> ERROR [2013-04-23 11:55:06,521] [BAMQueryReader.java:100]  Error querying
> BAM file
> java.lang.**ArrayIndexOutOfBoundsException**: 4683
>     at net.sf.samtools.**AbstractBAMFileIndex.query(**AbstractBAMFileIn
> dex.java:313)
>     at net.sf.samtools.**DiskBasedBAMFileIndex.**getSpanOverlapping(**Dis
> kBasedBAMFileIndex.java:55)
>     at net.sf.samtools.BAMFileReader.**createIndexIterator(**BAMFileRea
> der.java:521)
>     at net.sf.samtools.BAMFileReader.**query(BAMFileReader.java:288)
>     at net.sf.samtools.SAMFileReader.**query(SAMFileReader.java:346)
>
> Pawel
>
>
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