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VQSR with custom annotations?
Is it possible to run VQSR with custom annotations? I added some additional columns (not produced by GATK) to the INFO field of my VCF file, and included them with the "-an" flag to VariantRecalibrator. The VariantRecalibratorEngine reports convergence, but then I get this:
INFO 12:55:25,499 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000. ##### ERROR stack trace java.lang.IllegalArgumentException: No data found. at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:88) at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:408) at org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:156) at org.broadinstitute.gatk.engine.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
If I run VariantRecalibrator without the custom annotations but everything else the same, it works. I'm using GATK v3.4-46-gbc02625.