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Indel Variant recalibration is showing an error

NeethuNeethu IndiaMember

I have done joint genotyping of 200 samples and I have a multi sample vcf file. SNP recalibration worked but when I did Indel quality score recalibration it shows an 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"

I have used the below command
java -Xmx8g -XX:ParallelGCThreads=20 -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T VariantRecalibrator -R /mnt/exome/ReferenceFiles/human_g1k_v37.fasta -input recalibrated_snps_raw_indels.vcf -resource:mills,known=true,training=true,truth=true,prior=12.0 /mnt/exome/ReferenceFiles/Resource/Mills_and_1000G_gold_standard.indels.b37.vcf -an QD -an DP -an FS -an SOR -an ReadPosRankSum -an MQRankSum -mode INDEL -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 --maxGaussians 4 -recalFile recalibrate_INDEL.recal -tranchesFile recalibrate_INDEL.tranches -rscriptFile recalibrate_INDEL_plots.R

It would be really great if some one can help me to trouble shoot this.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited April 2017


    Can you try using dbSNP as well? It looks like you set the Mills resource file as known=true,training=true,truth=true which may be producing the error. Have a look at this article for information on what we recommend for indels in VQSR.


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