Hi GATK team,
I am using VariantAnnotator in GATK release (3.4, 3.6, 3.7) with command-line:
java -Xmx10g -jar $GATK -T VariantAnnotator \
-R $REF \
-V Input.vcf \
--resource:KGenomes $RESOURCE/ALL.WGS.chr.phase3_biallelic.vcf \
--expression oneKG.AF \
-o output.vcf
it prompts an error message as follows:
INFO 15:57:03,893 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:57:03,895 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 15:57:03,896 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 15:57:03,896 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 15:57:03,896 HelpFormatter - [Sat Dec 31 15:57:03 HKT 2016] Executing on Linux 2.6.32-279.el6.x86_64 amd64
INFO 15:57:03,897 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14
INFO 15:57:03,902 HelpFormatter - Program Args: -T VariantAnnotator -R /share_bio/unisvx3/zengchq_group/sohail/Ref/ref-1000G/hs37d5.fa -V /share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/SELECT_VAR/LD_PRUNING/PRE-PROCESS//VQSR_PHASE2_snp99.5-Combine_Biallelic-MAF-0.01-TIB_ONLY.vcf --resource:KGenomes /share_bio/unisvx3/zengchq_group/sohail/RawData/1000G/SLECTVAR//ALL.WGS.chr.phase3_biallelic.vcf --expression oneKG.AF -o /share_bio/unisvx3/zengchq_group/sohail/_SGDP-SAMPLES/GATK/ANALYSIS/TIB-EXCLUSIVE/PREPROCESS/VAR-ANNOTATE//VQSR_PHASE2_snp99.5-Combine_Biallelic-MAF-0.01-TIB_ONLY-UPDATE-1KGAF.vcf
INFO 15:57:03,907 HelpFormatter - Executing as sohail@node2 on Linux 2.6.32-279.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
INFO 15:57:03,908 HelpFormatter - Date/Time: 2016/12/31 15:57:03
INFO 15:57:03,908 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:57:03,909 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:57:03,940 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:57:04,110 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 15:57:04,796 GenomeAnalysisEngine - Preparing for traversal
INFO 15:57:04,810 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:57:04,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:57:04,812 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:57:04,812 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
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:316)
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 3.7-0-gcfedb67):
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 ------------------------------------------------------------------------------------------
Thanks for your help in advance!
Kind Regards