The current GATK version is 3.2-2

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

VCF from GenotypeGVCFs missing fields

Posts: 65Member

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
}

Tagged: