VariantsToVCF Error: Null alleles are not supported

Hi GATK team,

I am trying to convert HapMap output files of TASSEL3 to VCF using the GATK VariantsToVCF tool. However, I am getting the error below. I used GATK v3.2-2-gec30cee. Do the "null genotypes" refer to the N genotypes in the sample columns of HapMap? There are quite a lot of them. Should I omit these info? Is there a workaround to avoid the error?

Thanks!
Iris

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

ERROR stack trace

java.lang.IllegalArgumentException: Null alleles are not supported
at htsjdk.variant.variantcontext.Allele.(Allele.java:120)
at htsjdk.variant.variantcontext.Allele.create(Allele.java:211)
at htsjdk.variant.variantcontext.Allele.create(Allele.java:314)
at org.broadinstitute.gatk.engine.refdata.VariantContextAdaptors$HapMapAdaptor.convert(VariantContextAdaptors.java:380)
at org.broadinstitute.gatk.engine.refdata.VariantContextAdaptors.toVariantContext(VariantContextAdaptors.java:90)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.getVariantContexts(VariantsToVCF.java:179)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:127)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:87)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$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.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

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: Null alleles are not supported

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