error while running realignerTargetCreator

Question

[raya.girish]

Hello All I have sample obtain from Ion torrent machines I looking for somatic mutations I already did preprocessing of samples but when i am running RealignerTargetCreator its giving me error I am not able to tackle it please help The error is

ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: 1 at org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase(ReferenceContext.java:179) at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:212) at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:117) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):

ERROR

ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.

ERROR If not, please post the error message, with stack trace, to the GATK forum.

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions https://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: 1

ERROR ------------------------------------------------------------------------------------------

[WouterDeCoster]

The GATK forum might be a more appropriate place for this, in addition you probably should share the command you tried.

[Pierre Lindenbaum]

This errors occurs when there is a difference between the FASTA/chromosome sizes and the BED/BAM sizes.