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How to use the VQSR -tranche argument

WimSWimS Member Posts: 27

How should I use the VQSR -tranche argument?

From the tutorial I get that I should specify the list of doubles like this:
-tranche [100.0, 99.9, 99.0, 90.0]

But when I try that like this
java -jar GenomeAnalysisTK-2.6-3-gdee51c4/GenomeAnalysisTK.jar -T VariantRecalibrator -R ref.fa -input input.vcf -resource:snparray,known=true,training=true,truth=true,prior=15.0 input_concordantW_SNPArray.vcf -an QD -an ReadPosRankSum -an MQRankSum -an MQ -an FS -an DP -an ClippingRankSum -an BaseQRankSum -an AF -titv 2.5 --mode SNP -recalFile input.recal -tranchesFile input.tranches -rscriptFile input.plots.R -tranche [100.0, 99.9, 99.0, 90.0]

I get

`##### ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 2.6-3-gdee51c4):
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 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
ERROR MESSAGE: Invalid argument value '99.9,' at position 38.
ERROR Invalid argument value '99.0,' at position 39.
ERROR Invalid argument value '90.0]' at position 40.
ERROR ------------------------------------------------------------------------------------------`

Best Answer


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