Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.

Sign In or Register to comment.