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Values for QD annotation not detected for ANY training variant in the input callset.


I am running VariantRecalibrator on 2 WGS using the command:

gatk VariantRecalibrator \
-R ./hg38/Homo_sapiens_assembly38.fasta \
-V combinedgVCF.g.vcf.gz \
--resource hapmap,known=false,training=true,truth=true,prior=15.0:./hg38/hapmap_3.3.hg38.vcf.gz \
--resource omni,known=false,training=true,truth=false,prior=12.0:./hg38/1000G_omni2.5.hg38.vcf.gz \
--resource 1000G,known=false,training=true,truth=false,prior=10.0:./hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--resource dbsnp,known=true,training=false,truth=false,prior=2.0:./hg38/dbsnp_146.hg38.vcf.gz \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
-mode SNP \
--output /VQSR_test/output.recal \
--tranches-file /VQSR_test/output.tranches \
--rscript-file /VQSR_test/output.plots.R

The combined GVCF of the 2 WGS is produced using: HaplotypeCaller -ERC GVCF -> CombineGCVFs -> GenotypeGVCFs

The QD, MQ, MQRankSum, ReadPosRankSum, FS and SOR scores are present in all the variant calls in the input gvcf.

Why is "Values for QD annotation not detected for ANY training variant in the input callset." when I can see that they are present in the input callset? What am I doing wrong here?

Also, the tranches file is empty.

Hope you can help.

Kind regards,

Best Answer


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