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VQSR with custom annotations?

smgogartensmgogarten University of WashingtonMember

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.

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