GATK IndelRealigner Error:Code Exception

[HongxiangZheng]

Hi, all

Sorry to interrupt again.

I did some work on Local realignment around indels and followed the steps online.

The step 1 was ok.When I ran the 2nd command,An error appeared.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at org.broadinstitute.sting.utils.sam.AlignmentUtils.createIndelString(AlignmentUtils.java:669)
at org.broadinstitute.sting.utils.sam.AlignmentUtils.leftAlignIndel(AlignmentUtils.java:568)
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.determineReadsThatNeedCleaning(IndelRealigner.java:807)
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.clean(IndelRealigner.java:591)
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.cleanAndCallMap(IndelRealigner.java:463)
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.map(IndelRealigner.java:437)
at org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.map(IndelRealigner.java:68)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:101)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:49)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:67)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:103)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:97)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:244)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.4705):
##### ERROR
##### ERROR Please visit to wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------

The input file should be OK, for I ran validsamfile and only found some information" CIGAR should have zero elements for unmapped read", which was considered no problem in Pichard website. The input file is sorted.

Can anyone help?


Additional, I thought the problem might be:

1.those unmapped read have non zero elements in Cigar.
or

2 there might be invalid charactor such as "W" or "K" in reads.

Then, How can I remove those invalid reads or charactors?

[HongxiangZheng]

It seems solved.For those reads mapped off the end of the contig might cause the problem.

New version of GATK would solved it.
Thank Erik Banks @http://getsatisfaction.com/gsa/.