The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

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

Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

VCF from GenotypeGVCFs missing fields

dklevebringdklevebring Member Posts: 79

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.