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Has VariantAnnotator tool been removed from GATK

Hello, I am trying to run the following command with GATK 3-.8 without success. Has this tool been disabled?

Thanks

srun java -Xmx"$MEM"g -jar $GATK \
-R "$REFERENCE" \
-T VariantAnnotator \
--variant "$OUTPUT"All_samples_recalibrated_and_normalized_variants.vcf \
--useAllAnnotations \
--out "$OUTPUT"All_samples_recalibrated_and_normalized_variants.annot.vcf

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @simonsanchezj , that tool has not been removed. What is the error message you are getting?

  • KatieKatie United StatesMember ✭✭

    I cannot find this tool in GATK 4.0 either. Thank you!

  • simonsanchezjsimonsanchezj GermanyMember

    NFO 12:18:06,351 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 12:18:06,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
    INFO 12:18:06,356 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
    INFO 12:18:06,356 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
    INFO 12:18:06,357 HelpFormatter - [Thu Jan 11 12:18:06 CET 2018] Executing on Linux 2.6.32-504.8.1.el6.x86_64 amd64
    INFO 12:18:06,357 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13
    INFO 12:18:06,364 HelpFormatter - Program Args: -R Resources/hg19/ucsc.hg19.fasta -T VariantAnnotator --variant VCF_files/WES_FTD_2017/All_samples_recalibrated_and_normalized_variants.vcf --useAllAnnotations --out VCF_files/WES_FTD_2017/All_samples_recalibrated_and_normalized_variants.annot.vcf
    INFO 12:18:06,374 HelpFormatter - Executing as [email protected] on Linux 2.6.32-504.8.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13.
    INFO 12:18:06,375 HelpFormatter - Date/Time: 2018/01/11 12:18:06
    INFO 12:18:06,376 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 12:18:06,376 HelpFormatter - ----------------------------------------------------------------------------------
    ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/groups/owncloud_ftdgc/data/simonj/files/NGS_tools/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
    ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
    INFO 12:18:06,694 GenomeAnalysisEngine - Deflater: JdkDeflater
    INFO 12:18:06,695 GenomeAnalysisEngine - Inflater: JdkInflater
    INFO 12:18:06,696 GenomeAnalysisEngine - Strictness is SILENT
    INFO 12:18:06,924 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
    INFO 12:18:07,558 GenomeAnalysisEngine - Preparing for traversal
    INFO 12:18:07,571 GenomeAnalysisEngine - Done preparing for traversal
    INFO 12:18:07,572 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 12:18:07,573 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 12:18:07,573 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
    WARN 12:18:07,813 AS_RankSumTest - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,814 AS_StrandBiasTest - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,821 AS_RankSumTest - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,821 AS_RankSumTest - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,822 AS_RankSumTest - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,822 AS_RMSAnnotation - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,822 AS_RankSumTest - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,822 AS_StrandBiasTest - Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output
    WARN 12:18:07,828 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
    WARN 12:18:07,831 SnpEff - The SnpEff annotator requires that a SnpEff VCF output file be provided as a rodbinding on the command line via the --snpEffFile option, but no SnpEff rodbinding was found.
    WARN 12:18:07,831 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
    WARN 12:18:08,480 BaseQualitySumPerAlleleBySample - Annotation will not be calculated, can only be called from MuTect2, not VariantAnnotator
    WARN 12:18:08,481 AnnotationUtils - DP annotation will not be calculated, must be called from HaplotypeCaller or MuTect2, not VariantAnnotator
    WARN 12:18:08,482 OxoGReadCounts - Annotation will not be calculated, can only be called from MuTect2, not VariantAnnotator
    WARN 12:18:08,482 AnnotationUtils - SAC annotation will not be calculated, must be called from HaplotypeCaller or MuTect2, not VariantAnnotator
    WARN 12:18:08,482 AnnotationUtils - SB annotation will not be calculated, must be called from HaplotypeCaller or MuTect2, not VariantAnnotator

    ERROR --
    ERROR stack trace

    java.lang.IllegalStateException: ClusteredReadPosition: walker is not MuTect2
    at org.broadinstitute.gatk.tools.walkers.cancer.ClusteredReadPosition.annotate(ClusteredReadPosition.java:134)
    at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:230)
    at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:212)
    at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:355)
    at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotator.map(VariantAnnotator.java:112)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    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: ClusteredReadPosition: walker is not MuTect2
    ERROR ------------------------------------------------------------------------------------------

    srun: error: compute-05: task 0: Exited with exit code 1
    Thu Jan 11 12:18:08 CET 2018: GATK -> Variant fully annotated.
    Thu Jan 11 12:18:08 CET 2018: Apply hard filters to SNPs
    srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
    srun: got SIGCONT
    slurmstepd: *** STEP 55727.1 CANCELLED AT 2018-01-11T12:18:11 *** on compute-05
    slurmstepd: *** JOB 55727 CANCELLED AT 2018-01-11T12:18:11 *** on compute-05
    srun: forcing job termination

  • y_zhang88y_zhang88 Member
    edited January 2018

    Cannot find VariantAnnotator in GATK4 too. When I typed python gatk VariantAnnotator --help, I got this feedback:

    Exception in thread "main" org.broadinstitute.hellbender.exceptions.UserException: 'VariantAnnotator' is not a valid command.

        `at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:341)
        at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:172)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:192)
        at org.broadinstitute.hellbender.Main.main(Main.java:275)`
    
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited January 2018

    @simonsanchezj
    Hi,

    What happens if you remove --useAllAnnotations and just request one annotation?

    @y_zhang88 @Katie
    Hi,

    It looks like VariantAnnotator is not in GATK4. I will check if there are plans to port it.

    -Sheila

    EDIT: VariantAnnotator has not yet been ported to GATK4. It should be available soon.

  • pjongeneelpjongeneel Member
    edited January 2018

    Hey there @Sheila, I was wondering 2 things.

    If I used GATK4's haplotype caller - and added either -G arguments or -A arguments, can I skip VariantAnnotator step? I mean, does the output VCF essentially contain those annotations I specify with -A and VariantAnnotator tool is not necessary?

    Secondly, Haplotyper caller accepts -G for annotation groups. Things like AS_Standard and what not. Where can I find information as to what groups are available, and what annotation each group contains? I have looked over the GATK4 docs and cant seem to find that information.

    I'm specifically adding:
    -A RMSMappingQuality \
    -A MappingQualityRankSumTest \
    -A ReadPosRankSumTest \
    -A StrandOddsRatio \
    -A FisherStrand \
    -A QualByDepth

    to my gatk4 haploytypecaller command line.

    Lastly if you could point me to any documentation about specifying threads for many of these tools that would be great. Things like BQSR Recalibrator and ApplyBQSR I couldn't find out how to specify the number of threads to use, and nothing on default thread behavior (whether each tool uses a different amount of threads, 1, or all available, and how to modify the threading behavior for each tool)

    Post edited by pjongeneel on
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @pjongeneel
    Hi,

    If you specify the annotations you want with -A in HaplotypeCaller, you should not need to use VariantAnnotator. Have a look at this article for some tips.

    For the number of threads to specify, I think this article will help you.

    -Sheila

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