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PhasebyTransmission error concerning Genotype Likelihood score

JumaQuarJumaQuar Member
edited June 2013 in Ask the GATK team

Hello Team,

I am attempting to run GATK's PhasebyTransmission command to phase a vcf file contains a father, mother, son trio generated from complete genomics mkvcf command.

After creating the ped file and running the command I generate the error: "MESSAGE: BUG: Attempted to get likelihoods as strings and neither the vector nor the string is set!". I am not exactly sure what this means.

When I check my file and the documentation I am able to see that the 'GL' field is contained in the file, but could this not be the case? I have attached a few lines from the vcf I am using.

Any help with resolving the this issue would be of great help.

Thank you



Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    Can you please tell me what version of GATK you are using? Also, have you validated your VCF file?

  • GATK version: version 2.5-2-gf57256b

    I identified a few formatting errors from the CGI tools output that I corrected which allowed ValidateVariants to fully complete. When I tried to run the the phasebytransmission command I get this error:

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

    java.lang.ArrayIndexOutOfBoundsException: 1
    at org.broadinstitute.variant.variantcontext.GenotypeLikelihoods.getAsMap(
    at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.getLikelihoodsAsMapSafeNull(
    at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-gf57256b):
    ERROR Please check the documentation guide to see if this is a known problem
    ERROR If not, please post the error, with stack trace, to the GATK forum
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions
    ERROR ------------------------------------------------------------------------------------------

    I have attached my updated vcf file, any help would be greatly appreciated.

  • JumaQuarJumaQuar Member
    edited June 2013

    Also, here are the command and .ped file I am using.

    ped file:

    Family_63   GS000009556-ASM 0   0   1   2  
    Family_63   GS000009551-ASM 0   0   2   1  
    Family_63   GS000008961-ASM GS000009556-ASM GS000009551-ASM 1   2  


    java -Xmx1g -jar /home/dquarless/bin/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R /projects/stsi/data/GRCh37/GRCh37_p2/BWA_index/GRCh37.chr1_22_XYMT.fa -T PhaseByTransmission -V input.vcf -ped Family_63.ped -o Family_63_output.vcf
    Post edited by Geraldine_VdAuwera on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    OK, we'll have a look at this and try to debug it locally. I'll let you know what we find.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    FYI there are three line breaks in the vcf file you posted that shouldn't be there (lines 61-62, 71-72, 77-78). That's not the cause of your issue but next time please make sure that the data you give us is in good shape, otherwise it needlessly increases the time we spend debugging your issue...

  • This answer was amazing! Thank you for the help. Catching the validation pass would have been tricky.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Credit goes to Eagle Eyed Eric on this one :)

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