HaplotypeScore not annotated?
Posted in Ask the GATK team | Last updated on 2012-10-23 10:00:08


Comments (4)

Hi there, I'm running into an issue with my Queue pipeline, with variants called with HaplotypeCaller. Once I get the raw VCF file, I use VariantAnnotator before VQSR: however, no HaplotypeScore annotation is being produced, resulting in a failure of the VariantRecalibrator step where 'HaplotypeScore' was indicated as an annotation.

I tried to correct the issue by indicating to VariantAnnotator to use all annotations

  class AnnotationArguments (t: Target) extends VariantAnnotator with UNIVERSAL_GATK_ARGS {
this.reference_sequence = qscript.referenceFile
// Set the memory limit to 7 gigabytes on each command.
    this.memoryLimit = 7
    this.input_file :+= qscript.bamFile
    this.useAllAnnotations
    this.D = qscript.dbSNP_b37
  }

But I still can't get any output in the annotated VCF of that parameter. Here an example of a variant

 AC=5;AF=0.078;AN=64;ActiveRegionSize=179;ClippingRankSum=-0.568;DB;DP=2025;EVENTLENGTH=0;FS=4.139;InbreedingCoeff=-0.0847;MLEAC=5;MLEAF=0.078;MQ=69.98;MQRankSum=-1.428;NVH=1;NumHapAssembly=15;NumHapEval=13;QD=17.20;QDE=17.20;ReadPosRankSum=-1.762;TYPE=SNP;extType=SNP

Any suggestions on what I might be doing wrong?

thanks very much for your help, Francesco


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