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"Code exception" error with Haplotype Caller

Hi,
I am trying GATK v3.2-2 and HaplotypeCaller sometimes fails with the error stack copied below. It is not a consistent error - rerunning the same script again usually works fine, so it seems somewhat random when it fails. The errror stack is below:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException
at htsjdk.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:51)
at htsjdk.samtools.SAMRecordCoordinateComparator.compare(SAMRecordCoordinateComparator.java:41)
at java.util.TimSort.binarySort(TimSort.java:265)
at java.util.TimSort.sort(TimSort.java:208)
at java.util.TimSort.sort(TimSort.java:173)
at java.util.Arrays.sort(Arrays.java:659)
at java.util.Collections.sort(Collections.java:217)
at org.broadinstitute.gatk.utils.sam.ReadUtils.sortReadsByCoordinate(ReadUtils.java:320)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.finalizeActiveRegion(HaplotypeCaller.java:1172)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.referenceModelForNoVariation(HaplotypeCaller.java:1062)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:865)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Command arguments in this case were:
Program Args: -nct 8 -T HaplotypeCaller -R /tmp/pbs.7728727.cx1b/reference.fa -I /tmp/pbs.7728727.cx1b/realigned.recalibrated.bam -ERC GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o /tmp/pbs.7728727.cx1b/HCgenomic.vcf -rf BadCigar -L /tmp/pbs.7728727.cx1b/fragment.intervals

Many thanks,
Dalia

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