Hello,
Running VariantAnnotator, I am running into errors I couldn't find solutions for in the forum. Using the GnomAD publicly available VCF's, I would like to add information to a VCF, specifically frequency tracks (I am testing with a portion of chromosome 1 to test with). I am using the following command:
java -jar ~/Downloads/GenomeAnalysisTK38.jar -R ~/build/GRCh37/GRCh37.fa -T VariantAnnotator -V sample.vcf --comp:gnomad,vcf gnomad.vcf --expression gnomad.AF -o output_AF.vcf
The error I get is:
##### ERROR --
##### ERROR stack trace
java.lang.NullPointerException
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotator.initialize(VariantAnnotator.java:284)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------
If I remove the --expression command, it works perfectly fine and I get an output vcf with ";gnomad" added to the FORMAT column wherever the variant was observed in GnomAD (but ofcourse without any other GnomAD-derived annotation). The error occurs with any requested field (GT, DP, AC, AF, lcr, etc.).
I ran ValidateVariants on both VCF's. Both exited with "Done. There were no warn messages."
Thank you very much in advance for any help.
Klaasjan