[svtoolkit-help] error in discovery step: invalid cnp coordinates

[Verena T. <tis...@go...>]

Hi,

I am running GenomeSTRiP on eland mapped files and the preprocessing of
bams works fine.
However in the SVDiscovery step I end up with the following error

##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0009_3706
91702292 91702291
    at
org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198)
    at
org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166)
    at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599)
    at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405)
    at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
    at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
    at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
    at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
    at
org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
    at
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
    at
org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
    at
org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
    at
org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
    at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
    at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
    at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
##### 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: Invalid cnp coordinates: DEL_P0009_3706 91702292
91702291
##### ERROR
------------------------------------------------------------------------------------------


This error occurs only for one chromosome, all other chromosomes run fine

Thanks a lot for your help
Verena