Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

Best Answer


Sign In or Register to comment.