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.

VariantRecalibrator error

I am trying to run the Germline short variant discovery using GATK4 and following the steps found on: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145
everything runs ok until i reach the end where i\m supposed to run the VariantRecalibrator
the command is something like:

java -Xmx10g -jar /home/Downloads/gatk- \VariantRecalibrator --max-gaussians 4 \-R hg38.fa \-V myOutput.g.vcf \--resource known=false,training=true,truth=true,prior=15.0:hapmap_3.3.hg38.vcf.gz \--resource known=false,training=true,truth=false,prior=10.0:1000G_phase1.snps.high_confidence.hg38.vcf.gz \--resource known=false,training=true,truth=false,prior=12.0:1000G_omni2.5.hg38.vcf.gz \--resource known=true,training=true,truth=false,prior=2.0:Homo_sapiens_assembly38.dbsnp138.vcf.gz \-an GT \-mode SNP \-O output.recal \--tranches-file output.tranches \--rscript-file output.plots.R

where myOutput.g.vcf is the outout file from running HaplotypeCaller in gvcf mode

and i am getting the following error

A USER ERROR has occurred: Bad input: Values for GT annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.

I tried running VariantAnnotator first but the same error keeps on showing


Sign In or Register to comment.