We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

--resource not being seen in VariantRecalibrator

apolyakapolyak State College, PA, USAMember

Hi All. For some reason I'm getting this error message when running GATK 3.3 VariantRecalibrator:


ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
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 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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Argument '--resource' requires a value but none was provided
ERROR ------------------------------------------------------------------------------------------

java -d64 -Xmx8g -jar $GATKDIR/GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-input b37.vcf \
-R $REF \
-resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 $HAPMAP \
-resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 $OMNI \
-resource:dbsnp,VCF,known=true,training=false,truth=false,prior=8.0 $DBSNP \
-resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 $MILLS \
-an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ \
--mode BOTH \
-recalFile b37.recal \
-tranchesFile b37.tranches \
-rscriptFile b37.R \
-nt 6 --TStranche 100.0 --TStranche 99.9 --TStranche 99.5 --TStranche 99.0 \
--TStranche 98.0 --TStranche 97.0 --TStranche 96.0 --TStranche 95.0 --TStranche 94.0 \
--TStranche 93.0 --TStranche 92.0 --TStranche 91.0 --TStranche 90.0

I checked to see if the resource files exists, and they do. I cannot seem to figure out what the problem is.

Any help will be much appreciated

Best Answer


Sign In or Register to comment.