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No Tribble Error when running Variant Recalibrator

We are trying to get the Variant Recalibrator to run, but keep getting a "No tribble type" error.

Here are the commands we are running:

java -Xmx2g -jar /data/homes/kamensh/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T VariantRecalibrator -R /data/Ehringer/Helen/Genome/hg19.fixed.fasta --input /data/Ehringer/Helen/Processing/BWA/VCF/UCB_97.bwa.SNP.vcf --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /data/homes/kamensh/hapmap_3.3.b37.sites.vcf --resource:omni,known=false,training=true,truth=false,prior=12.0 /data/homes/kamensh/1000G_omni2.5.b37.sites.vcf --resource:dbsnp,known=true,training=false,truth=false,prior=6.0 /data/homes/kamensh/dbsnp_135.b37.vcf --resource:mills,known=false,training=true,truth=true,prior=12.0 /data/homes/kamensh/Mills_and_1000G_gold_standard.indels.b37.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff --mode SNP --recal_file /data/Ehringer/Helen/Processing/BWA/VQSR/output.recal --tranches_file /data/Ehringer/Helen/Processing/BWA/VQSR/output.tranches --rscript_file /data/Ehringer/Helen/Processing/BWA/VQSR/output.plots.R

And the error we are getting:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.3-9-ge5ebf34):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
ERROR Name FeatureType Documentation
ERROR BCF2 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_bcf2_BCF2Codec.html
ERROR VCF VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
ERROR VCF3 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_vcf_VCF3Codec.html
ERROR ------------------------------------------------------------------------------------------

Any help you can give us would be greatly appreciated!

Answers

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