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Facing error while trying to build SNP recalibration model

discoveradnandiscoveradnan PakistanMember
edited January 2016 in Ask the GATK team

Hello everyone,

Kindly help me in fixing following error while trying to build SNP recalibration model,

$ java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Reference/hg19.fa -input raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /Reference/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /Reference/1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /Reference/1000G_phase1.snps.high_confidence.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /Reference/dbsnp_138.hg19.vcf -an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile recalibrate_SNP.recal -tranchesFile recalibrate_SNP.tranches -rscriptFile recalibrate_SNP_plots.R

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid argument value '-resource:hapmap known=false training=true truth=true prior=15.0' at positi

on 6.

ERROR Invalid argument value '/Reference/hapmap_3.3.hg19.vcf' at position 7.
ERROR Invalid argument value '-resource:omni known=false training=true truth=true prior=12.0' at position 8.
ERROR Invalid argument value '/Reference/1000G_omni2.5.hg19.vcf' at position 9.
ERROR Invalid argument value '-resource:1000G known=false training=true truth=false prior=10.0' at position 10.
ERROR Invalid argument value '/Reference/1000G_phase1.snps.high_confidence.hg19.vcf' at position 11.
ERROR Invalid argument value '-resource:dbsnp known=true training=false truth=false prior=2.0' at position 12.
ERROR Invalid argument value '/Reference/dbsnp_138.hg19.vcf' at position 13.
ERROR ------------------------------------------------------------------------------------------

Thanks and Best Regards,
Adnan

Answers

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