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ERROR MESSAGE: QD annotation at VariantRecalibrator


I am encountering an issue while using GATK 3.8 at VariantRecalibrator stage. Executed the following

java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -input /gatk_out/output.vcf --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /gatk/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf.gz --resource:omni,known=false,training=true,truth=false,prior=12.0 /gatk/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz --resource:1000G,known=false,training=true,truth=false,prior=10.0 /gatk/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /ncbi/00-All.vcf.gz -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP -recalFile /gatk_out/output.recal -tranchesFile /gatk_out/output.tranches -rscriptFile /gatk_out/output.plots.R

Error Message

##### ERROR MESSAGE: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.

Here, output.vcf is the output of GenotypeGVCFs command run on g.vcf files from mother, father and the child.
The hapmap, omni and 1000G files are downloaded from gatk resource.
The dbsnp file is downloaded from ncbi (dbsnp file from gatk resource gave an error).

I tried running VariantAnnotator in this way

java -jar GenomeAnalysisTK.jar -T VariantAnnotator -A QualByDepth -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -V /gatk_out/output.vcf -o /gatk_out/output_annotated.vcf

...changing output.vcf to output_annotated.vcf in the VariantRecalibrator command.

New Error

##### ERROR MESSAGE: Invalid command line: Argument annotation has a bad value: Annotation QD was not found; please check that you have specified the annotation name correctly

Can you please help ?


  • AdelaideRAdelaideR Member admin

    HI @lakhujanivijay Thanks for posting a question, we have been in a conference for the last two days which may have delayed your response. I see a very similar question has been asked in Biostars and that an answer has been accepted by the user. Are you one and the same?

    It seems that the crux of the problem was a mismatch in reference to snp files from the resource bundle. The latest and best version of the resource bundle can be downloaded from this google bucket referenced here.

    The Google cloud bucket is slightly more up to date. Please check out these links and let us know if this resolves the error.

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