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VQSR went wrong when recalibrating INDELs

EmmaDanEmmaDan ChinaMember


I try to run VQSR on my VCF file produced by HaplotypeCaller. It worked pretty well when dealing with SNPs, but errors prompted up when recalibrating INDELs. I am running GATK version3.2. Commend lines are below:

/ifs2/BC_MD/DEV/WorkFlow/Sofware/jre1.7.0_45/bin/java -Xmx5g -jar /ifs2/BC_MD/DEV/WorkFlow/Sofware/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -T VariantRecalibrator -R /ifs2/BC_MD/DEV/WorkFlow/Data/bundle_2.8_hg19/ucsc.hg19.fasta -input ./mem_with_a/HC_raw.vcf -resource:mills,known=true,training=true,truth=true,prior=12.0 /ifs2/BC_MD/DEV/WorkFlow/Data/bundle_2.8_hg19/Mills_and_1000G_gold_standard.indels.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /ifs2/BC_MD/DEV/WorkFlow/Data/bundle_2.8_hg19/dbsnp_138.hg19.vcf -an QD -an FS -an ReadPosRankSum -an MQRankSum -mode INDEL --maxGaussians 4 -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile ./mem_with_a/HC_indel.VQSR.recal -tranchesFile ./mem_with_a/HC_indel.VQSR.tranches

/ifs2/BC_MD/DEV/WorkFlow/Sofware/jre1.7.0_45/bin/java -Xmx5g -jar /ifs2/BC_MD/DEV/WorkFlow/Sofware/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -T ApplyRecalibration -R /ifs2/BC_MD/DEV/WorkFlow/Data/bundle_2.8_hg19/ucsc.hg19.fasta -input ./mem_with_a/HC_raw.vcf -mode INDEL --ts_filter_level 99.0 -recalFile ./mem_with_a/HC_indel.VQSR.recal -tranchesFile ./mem_with_a/HC_indel.VQSR.tranches -o ./mem_with_a/HC_indel.vcf

Error messages are there:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: No data found.
at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(
at org.broadinstitute.gatk.engine.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: No data found.
ERROR ------------------------------------------------------------------------------------------

Thank you!


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