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VQSR error - no MQ annotation detected
Hi, I am trying to run VQSR and an error occurred.
Here are my commands
java -Xmx240g -jar GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-R /ref/ucsc.hg19.fasta \
-input input_raw.vcf \
-recalFile snp.recal.vcf \
-tranchesFile snp.tranches \
-rscriptFile recalibrate_SNP_plots.R \
-nt 8 \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 /ref/hapmap_3.3.hg19.sites.vcf \
-resource:omni,known=false,training=true,truth=true,prior=12.0 /ref/1000G_omni2.5.hg19.sites.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 /ref/1000G_phase1.snps.high_confidence.hg19.sites.vcf \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /ref/dbsnp_138.hg19.vcf \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff \
-mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
and error messages.
ERROR MESSAGE: Bad input: Values for MQ annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
However, there MQ are annotated in my input files. Sample size is large enough (around 150 individuals) for VQSR and a combined vcf file of these samples has around 280,000 variants (it's exome data). Genome build version checked with my input data and reference, and GATK version is 3.5
I know similar errors have been reported before, but couldn't find the right solution.