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VCF from GenotypeGVCFs missing fields

So I've just run GenotypeGVCFs and get some odd looking things. The FORMAT field is GT:AD:DP:GQ:PL and on most occasions, the values are 1/1:0,1,0:1:3:10,3,0, i.e. 5 fields. However, sometimes I get ./.:.:317, only 3 fields.

I use queue to run this, so my case class is this:

case class genotypeGVCF(gvcfs:List[File], outvcf:File) extends GenotypeGVCFs with ExternalCommonArgs with FourteenCoreJob with NineDayJob {
    @Input(doc="list of gvcfs to merge") val inGVCFs = gvcfs
    @Output(doc="SNP calls in VCF format") val outVCF = outvcf
    this.variant = inGVCFs
    this.out = outVCF
    this.R = refGenome
    this.dbsnp = dbSNP
    this.jobName = "genotypeGVCF " + outvcf.getName()
    this.analysisName = this.jobName
    this.isIntermediate = false
    this.nt = 14
    this.intervals = Seq(targetIntervals)
    this.memoryLimit = 112
  }  

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