HaplotypeScore not annotated?

flescai

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

ebanks

Exactly. The Haplotype Score is inherently embedded inside the guts of the Haplotype Caller, which means it's no longer an appropriate annotation for that tool.

ebanks

Hi Francesco,

Our recommendation is that you follow the best practices for variant detection. It looks like you aren't doing that in your pipeline. That being said, you can always use the Variant Annotator to add the Haplotype Score to your VCF records if you really want to do that.

flescai

Hi Eric, thanks very much, I didn't quite notice the covariates changed in the new best practice to

 -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff -an ClippingRankSum

thanks for flagging it up! before using "this.useAllAnnotations" I used

 this.annotation ++= List("QD", "QDE", "HaplotypeScore", "MQRankSum", "ReadPosRankSum", "FS", "MQ")

but 'HaplotypeScore' was not added anyway. is that because of the output of HaplotypeCaller is different?

thanks for your help, Francesco

rpoplin

In the upcoming release of GATK v2.2 we restored this functionality and so you'll be getting HaplotypeScore again in your variant calls!

Cheers,