PhaseByTransmission Code Exception error

I used vcf file generated by other software, e.g. samtools mpileup,as input file for PhasebyTransmission. I got the Code exeception error message. I am wondering if this is due to the vcf INFO difference between GATK UnifiedGenotyper generated vcf files and other software generated vcf files. If yes, is there any solution to fix the vcf file generated from third party tools?
Here is the detailed error message.


INFO 16:54:51,589 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:54:51,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-13-g0f021e6, Compiled 2012/10/12 17:51:55
INFO 16:54:51,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:54:51,593 HelpFormatter - For support and documentation go to
INFO 16:54:51,594 HelpFormatter - Program Args: -T PhaseByTransmission -R X_GENOME.fa -V myfile.vcf -o test_phasebytrans.vcf -ped myfam.ped
INFO 16:54:51,594 HelpFormatter - Date/Time: 2013/04/18 16:54:51
INFO 16:54:51,594 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:54:51,595 HelpFormatter - ---------------------------------------------------------------------------------
INFO 16:54:51,635 ArgumentTypeDescriptor - Dynamically determined type of myfile.vcf to be VCF
INFO 16:54:51,643 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:54:51,723 RMDTrackBuilder - Loading Tribble index from disk for file myfile.vcf
WARN 16:54:51,983 RMDTrackBuilder - Index file myfile.vcf.idx is out of date (index older than input file), deleting and updating the index file
INFO 16:54:51,986 RMDTrackBuilder - Creating Tribble index in memory for file myfile.vcf
INFO 16:55:12,582 RMDTrackBuilder - Writing Tribble index to disk for file myfile.vcf.idx
INFO 16:55:23,778 PedReader - Reading PED file myfam.ped with missing fields: []
INFO 16:55:23,950 PedReader - Phenotype is other? false
INFO 16:55:24,267 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining

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

at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.getLikelihoodsAsMapSafeNull(
at org.broadinstitute.sting.gatk.walkers.phasing.PhaseByTransmission.phaseTrioGenotypes(
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.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 2.1-13-g0f021e6):
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
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR -------------------------------------------------------------

Best Answer


  • CarlaCarla Member
    edited April 2013
    Thank you! It's helpful by running ValidateVariants. I have another question, is PL required for phasebyTransmission? I have a vcf file does not have the PL info. It was validated by ValidateVariants but still was threw out with the error message code exception. Thanks.
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I don't think that's the problem. If the problem was that PL was required, then it would specifically say that in the error message.

    I see in the console output there is a line saying Reading PED file myfam.ped with missing fields: [] INFO 16:55:23,950 PedReader - Phenotype is other?. That may indicate that your PED file is not properly formatted. You should check that.

    Have you updated to the latest version? Among other things we have improved the error messages so it is easier to understand what is going wrong.

  • CarlaCarla Member
    edited April 2013

    Thanks. I do not think it's the ped file problem. One vcf file, which was generated from another pipe, went through PhasebyTransmission without any problem using the same ped. However, I got the same ped missing filed error message. I put 0 as phenotype. Here is my ped file

    FM1     M    0       0       2       0
    FM1     F  0       0       1       0
    FM1     C      M    F  0       0

    Currently, I could not update a new version. We do not have the full version license yet. Before any further testing with the Lite version, one thing I would like to make sure . Is the Lite version still free for profit users? Thank you!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, I see. Yes, the Lite version is still free for use for commercial users, but unfortunately we can't provide support for it because we only support the most recent versions.

    I guess you could try adding the PL field to your vcf file that lacks it, using VariantAnnotator, just in case that is indeed the problem. But you'll need the original bam file that was used to generate that vcf file in order to do so.

  • CarlaCarla Member

    Thank you very much!

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