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VariantRecalibrator Error: Values for QD annotation not detected for ANY training variant

nb82nb82 United StatesMember

I get the following error with VariantRecalibrator when I run it:

java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Os_nipponbare_v7.0_genome.fasta -input ESSR.vcf -mode SNP -recalFile ERS468243.raw.snps.recal -tranchesFile ERS468243.raw.snps.tranches -rscriptFile ERS468243.recal.plots.R -resource:dbSNP,known=true,training=true,truth=true,prior=6.0 all_sorted.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ

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.

What am I doing wrong? Am I using the wrong annotation?
Thanks in advance for any help.

Best Answer


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