VariantsToVCF Error: Null alleles are not supported

IrisUyIrisUy PhilippinesMember

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 ------------------------------------------------------------------------------------------

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @IrisUy
    Hi Iris,

    Can you please try running the latest version of GATK and see if the error persists?

    Thanks,
    Sheila

  • Im having the same issue with 3.5, having removed all but bi-allelic sites from Tassel HapMap output.

    INFO  11:26:40,804 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
    INFO  11:26:40,804 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  11:26:40,804 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO  11:26:40,808 HelpFormatter - Program Args: -T VariantsToVCF -dt NONE -R PS1_1.68.5.fasta -o ./East12_CHR9.vcf --variant:RawHapMap ./01_RawSNPs/East12_5lanes_MgTaxa_chr9.head.hapmap
    INFO  11:26:40,819 HelpFormatter - Executing as cfljam@aklbld31.pfr.co.nz on Linux 3.10.0-327.10.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14.
    INFO  11:26:40,819 HelpFormatter - Date/Time: 2016/06/14 11:26:40
    INFO  11:26:40,819 HelpFormatter - --------------------------------------------------------------------------------
    INFO  11:26:40,820 HelpFormatter - --------------------------------------------------------------------------------
    INFO  11:26:40,893 GenomeAnalysisEngine - Strictness is SILENT
    INFO  11:26:40,986 GenomeAnalysisEngine - Downsampling Settings: No downsampling
    INFO  11:26:41,047 RMDTrackBuilder - Writing Tribble index to disk for file /powerplant/workspace/cfljam/GBS/12East/standardGBS/30.GBS_PS1/./01_RawSNPs/East12_5lanes_MgTaxa_chr9.head.hapmap.idx
    INFO  11:26:41,120 GenomeAnalysisEngine - Preparing for traversal
    INFO  11:26:41,123 GenomeAnalysisEngine - Done preparing for traversal
    INFO  11:26:41,123 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO  11:26:41,124 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
    INFO  11:26:41,124 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
    INFO  11:26:42,665 GATKRunReport - Uploaded run statistics report to AWS S3
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
    java.lang.IllegalArgumentException: Null alleles are not supported
        at htsjdk.variant.variantcontext.Allele.<init>(Allele.java:139)
        at htsjdk.variant.variantcontext.Allele.create(Allele.java:234)
        at htsjdk.variant.variantcontext.Allele.create(Allele.java:355)
        at org.broadinstitute.gatk.utils.refdata.VariantContextAdaptors$HapMapAdaptor.convert(VariantContextAdaptors.java:246)
        at org.broadinstitute.gatk.utils.refdata.VariantContextAdaptors.toVariantContext(VariantContextAdaptors.java:89)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.getVariantContexts(VariantsToVCF.java:179)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:127)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:87)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$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:315)
        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:106)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    ##### 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 ------------------------------------------------------------------------------------------
    

    Issue · Github
    by Sheila

    Issue Number
    990
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @JohnMcCallum @IrisUy
    Hi

    Let me check with the team and get back to you.

    -Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Can you show a few records from your input files?
  • oz_ddpscoz_ddpsc St louisMember

    I have the same issue as above with the current 3.7 version of GATK. I have attached snippets of the error output and hapmap file.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Can you post an individual vcf record that reproduces the error?
  • blackFireflyblackFirefly Member
    edited July 2017

    Hi, I also want to convert an output file from TASSEL to VCF and got the same error, but with a different stack trace:

    ERROR --
    ERROR stack trace

    java.lang.IllegalArgumentException: Null alleles are not supported
    at htsjdk.variant.variantcontext.Allele.(Allele.java:139)
    at htsjdk.variant.variantcontext.Allele.create(Allele.java:234)
    at htsjdk.variant.variantcontext.Allele.create(Allele.java:355)
    at org.broadinstitute.gatk.utils.refdata.VariantContextAdaptors$HapMapAdaptor.convert(VariantContextAdaptors.java:246)
    at org.broadinstitute.gatk.utils.refdata.VariantContextAdaptors.toVariantContext(VariantContextAdaptors.java:89)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.getVariantContexts(VariantsToVCF.java:179)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:127)
    at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToVCF.map(VariantsToVCF.java:87)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$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:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
    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 https://software.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Null alleles are not supported
    ERROR ------------------------------------------------------------------------------------------

    Here is a record of my file (header line and one record):

    rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode aeth_2 aeth_1 aeth_12 aeth_15 aeth_17 aeth_6 aeth_16 aeth_19 aeth_CYP-1 aeth_119 aeth_11 aeth_118 aeth_117 aeth_10 aeth_238 aeth_116 aeth_237 aeth_115 aeth_235 aeth_234 aeth_113 aeth_112 aeth_233 aeth_111 aeth_232 aeth_231 aeth_110 aeth_230 aeth_9 aeth_8 aeth_109 aeth_108 aeth_229 aeth_228 aeth_106 aeth_227 aeth_226 aeth_105 aeth_225 aeth_103 aeth_223 aeth_102 aeth_222 aeth_101 aeth_100 aeth_220 aeth_34 aeth_37 aeth_36 aeth_39 aeth_31 aeth_219 aeth_30 aeth_218 aeth_33 aeth_32 aeth_216 aeth_214 aeth_213 aeth_212 aeth_211 aeth_210 aeth_24 aeth_26 aeth_25 aeth_28 aeth_209 aeth_208 aeth_20 aeth_207 aeth_22 aeth_21 aeth_205 aeth_204 aeth_203 aeth_202 aeth_201 aeth_57 aeth_59 aeth_58 aeth_51 aeth_53 aeth_55 aeth_46 aeth_45 aeth_48 aeth_47 aeth_49 aeth_TUR-1 aeth_40 aeth_42 aeth_41 aeth_44 aeth_78 aeth_71 aeth_70 aeth_73 aeth_72 aeth_75 aeth_74 aeth_77 aeth_76 aeth_80 aeth_68 aeth_67 aeth_69 aeth_60 aeth_62 aeth_61 aeth_64 aeth_63 aeth_66 aeth_93 aeth_92 aeth_95 aeth_97 aeth_96 aeth_99 aeth_98 aeth_199 aeth_198 aeth_195 aeth_194 aeth_193 aeth_192 aeth_190 aeth_82 aeth_84 aeth_83 aeth_86 aeth_85 aeth_88 aeth_87 aeth_189 aeth_188 aeth_91 aeth_187 aeth_186 aeth_90 aeth_185 aeth_184 aeth_183 aeth_182 aeth_181 aeth_180 aeth_179 aeth_178 aeth_177 aeth_175 aeth_174 aeth_173 aeth_172 aeth_171 aeth_168 aeth_167 aeth_166 aeth_165 aeth_164 aeth_163 aeth_162 aeth_161 aeth_160 aeth_159 aeth_158 aeth_157 aeth_156 aeth_154 aeth_153 aeth_152 aeth_150 aeth_149 aeth_148 aeth_147 aeth_144 aeth_143 aeth_142 aeth_141 aeth_140 aeth_139 aeth_138 aeth_137 aeth_136 aeth_132 aeth_130 aeth_129 aeth_127 aeth_125 aeth_124 aeth_123 aeth_121 aeth_241 aeth_120
    scsc-1_gi_9_1=S C/A csc-1_gi_9_1=Scaffold_1977=gi_9_2 46866 + NA NA NA NA NA NA N A N C C C C N A C A N C N N A N N C C C C A A C C N A N A A C N C C C A C C C A A A N A A C A N C C C C A A N N N A C A C A A A C C C A N N A A A A C N C C N A A C A N A A C C A C C A N C A A C C A C C A C C A C C A A C N N C A N C A C C C A N C A A C N N N A C A A A C N A N N A N A C C C C A A A C C C C N C A A A N C A A A C A A C A C C N C C A A C N A N N C A N C A A A C M A C

    I used the version: version 3.7-0-gcfedb67

    Issue · Github
    by Sheila

    Issue Number
    2333
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @blackFirefly
    Hi,

    Sorry for the delay. We have been away at a workshop. Let me check with the team and get back to you.

    -Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Unfortunately this tool cannot handle null genotypes, as indicated in the error message. We currently do not have any plans to extend this functionality, as we are moving away from supporting many different formats. You will need to find another tool to do the conversion.

  • blackFireflyblackFirefly Member
    edited August 2017

    Thank you for your answer. I used another tool for the conversion (:

    However, I am interested in understanding this "null genotypes" thing. What is the problem with the file? What is missing? (I've never worked with HapMap files before, so I don't know)

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @blackFirefly
    Hi,

    GATK tools only accept A,T,G,C alleles. Notice in your file, you have N or NA. I think those are the offending alleles.

    -Sheila

  • Oh, that's what the error ment. Thank you very much! (:

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