Test-drive the GATK tools and Best Practices pipelines on Terra
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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-220.127.116.11/gatk-package-18.104.22.168-local.jar \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