The following error is observed when running VariantRecalibrator with the --truth-sensitivity-tranche argument.
A USER ERROR has occurred: Argument truth-sensitivity-tranche has a bad value: [100.0,. Problem constructing Double from the string '[100.0,'.
My run statement is
./gatk VariantRecalibrator --reference $reference --variant $VCF --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /path/hapmap_3.3.b37.vcf --resource:omni,known=false,training=true,truth=true,prior=12.0 /path/1000G_omni2.5.b37.vcf --resource:1000G,known=false,training=true,truth=false,prior=10.0 /path/1000G_phase1.snps.high_confidence.b37.vcf --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /path/dbsnp_138.b37.vcf --use-annotation QD --use-annotation MQRankSum --use-annotation ReadPosRankSum --use-annotation FS --use-annotation MQ --use-annotation InbreedingCoeff --mode SNP --truth-sensitivity-tranche [100.0, 99.9, 99.0, 90.0] --output ${prefix}.SNP.recal --tranches-file ${prefix}.SNP.tranches --rscript-file ${prefix}.SNP.R
This error has been reproducible with both the local downloaded executable of GATK4 and the docker image, broadinstitute/gatk:latest. The argument was also passed exactly as listed on the formal documentation page for Variant Recalibrator.
--truth-sensitivity-tranche, -tranche [100.0, 99.9, 99.0, 90.0]
The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent).