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