Re: [svtoolkit-help] "Invalid sequence position"

[Bob H. <han...@br...>]

Including the stack trace would be most helpful.
If you are using an hg19-based reference, then chr17 is only 81195210 long.
Does ValidateSamFile like this bam?
This may be related to the bwa idiosyncracy of occasionally leaving 
nominally-invalid POS fields in unmapped records.
If so, I will try to fix it if you can send me the command line and 
stack trace.
-Bob

On 5/23/13 10:21 AM, John Broxholme wrote:
> Pre-processing of one(of 270+) deep BAM files has failed with:
>
> ...
> INFO Â 12:54:38,366 ComputeGCProfiles - Processing input file 
> org.broadinstitute.sv.dataset.SAMFileLocation@986cff74 ...Â
> Exception in thread "main" java.lang.RuntimeException: Invalid 
> sequence position: 17:81195230
> ...
>
> Where would this have come from?  The pipeline has been the same to 
> prepare all 270+ of the (25x deep) BAMs, and this is the only failure. 
> Â Any suggestions on what might be wrong and how to fix it will be 
> most welcome!
>
> Thanks
> John
>
> -- 
> John Broxholme
> Wellcome Trust Centre for Human Genetics
> Roosevelt Drive, Oxford, OX3 7BN, UK
>
>
>
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