NullPointerException in HaplotypeCaller for RNAseq

Hi,

I was trying to call variants in RNAseq data using GATK 3.0 when I got the following stack trace:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.NullPointerException
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:421)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:395)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.calculateGLsForThisEvent(GenotypingEngine.java:385)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:222)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:872)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:141)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
        at org.broadinstitute.sting.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 nightly-2014-03-10-gf78001a):
##### 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 ------------------------------------------------------------------------------------------

Here are the command line arguments:

Program Args: -T HaplotypeCaller -I in.bam -R ref.fa -o raw.snps.indels.vcf -nct 8 -recoverDanglingHeads -dontUseSoftClippedBases -stand_call_conf 20 -stand_emit_conf 20

As you can see, I got the error above from one of the nightly builds. Before that I also tried version 3.0-0-g6bad1c6, and this produced the exact same error. What's curious about this is that it didn't fail in the same place each time. I did this on 20 samples, and for the first run, 15 of the samples failed with this error. One of the samples failed after 7 minutes, so I decided to try that one again to see if I could reproduce it, but it went past the point (both in time and genomic position) where it failed the first time.

I decided to download a nightly build (version nightly-2014-03-10-gf78001a) and see if this had been fixed, but again, 15 of the samples failed. However, it was not the same set of samples that failed as with the other version.

The reads were aligned using STAR, and prior to this step I ran SplitNCigarReads and IndelRealigner.

Thanks, Niklas