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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

ArrayIndexOutOfBoundsException in HaplotypeCaller

Command was:
java -Xmx4g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ref.fasta -I sample1.cleaned.sorted.rmdup.realigned.bam -o sample1.haplo.vcf

UnifiedGenotyper works with the same input

pao205@bio-masago:~/tmp/indel$ gatk -T HaplotypeCaller -R ramorum1.fasta -I 12475.cleaned.sorted.rmdup.realigned.bam -o 12475.haplo.vcf
INFO 16:55:17,314 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:55:17,317 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-7-g5e89f01, Compiled 2013/03/06 01:01:28
INFO 16:55:17,318 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:55:17,318 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:55:17,323 HelpFormatter - Program Args: -T HaplotypeCaller -R ramorum1.fasta -I 12475.cleaned.sorted.rmdup.realigned.bam -o 12475.haplo.vcf
INFO 16:55:17,324 HelpFormatter - Date/Time: 2013/03/13 16:55:17
INFO 16:55:17,324 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:55:17,324 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:55:17,409 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:55:17,935 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 16:55:17,944 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:55:18,041 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
INFO 16:55:18,785 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files
INFO 16:55:18,834 GenomeAnalysisEngine - Done creating shard strategy
INFO 16:55:18,834 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:55:18,834 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining
INFO 16:55:48,838 ProgressMeter - scaffold_1:36910 1.64e+04 30.0 s 30.5 m 0.1% 15.0 h 15.0 h
INFO 16:56:48,839 ProgressMeter - scaffold_1:53293 4.92e+04 90.0 s 30.5 m 0.1% 31.3 h 31.2 h
...
INFO 21:54:49,518 ProgressMeter - scaffold_11:611973 9.37e+06 5.0 h 32.0 m 14.1% 35.5 h 30.5 h
INFO 21:55:49,636 ProgressMeter - scaffold_12:400 9.46e+06 5.0 h 31.8 m 14.2% 35.3 h 30.3 h
INFO 21:56:38,764 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: -1
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.generateVCsFromAlignment(GenotypingEngine.java:675)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:140)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:500)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:132)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:552)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:512)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:244)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:69)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-7-g5e89f01):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
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