When running GATK, I am getting "empty" results when running BaseRecalibrator. I didn't see a solution to this when searching.
java -Xmx4g -jar /seqprg/GenomeAnalysisTK-2.4-3-g2a7af43/GenomeAnalysisTK.jar -l INFO -R /Users/bcantarel/projects/refdb/human_g1k_v37.fasta --knownSites /Users/bcantarel/projects/refdb/00-All.vcf -I Sample_cDNA405.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o Sample_cDNA405.grp
java.lang.IllegalStateException: recalibration tables list is empty at org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationEngine.mergeThreadLocalRecalibrationTables(RecalibrationEngine.java:209) at org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationEngine.finalizeData(RecalibrationEngine.java:175) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:508) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.onTraversalDone(BaseRecalibrator.java:131) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:123) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
