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The mutect ERROR:Please add an explicit type tag :NAME listing the correct type from among the supported types

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    Genevieve Brandt (she/her)

    Hello,

    In GATK 4.2.0.0 we only support Mutect2. There are many improvements from Mutect1 to Mutect2 so we recommend that you use the updated version.

    Here is our support policy for more details: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines

    Please let us know if updating to Mutect2 does not solve your issue!

    Best,

    Genevieve

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    灵己 孟

    Dear professors,I also try to recheck my version.

    GATK:The Genome Analysis Toolkit (GATK) v3.1-0-g72492bb

    Mutect:mutect-1.1.7.jar

    java:1.7.0_80

     

    The whole scrennprint is as follows,

    java -Xmx31g -jar /home/xxzhang/workplace/QBRC//somatic_script/mutect-1.1.7.jar --analysis_type MuTect --reference_sequence ./geneome/hg19/hg19.fa --dbsnp ./geneome/hg19/hg19.fa_resource/dbsnp.hg19.vcf --cosmic ./geneome/hg19/hg19.fa_resource/CosmicCodingMuts.hg19.vcf --input_file:tumor /home/xxzhang/workplace/output/tumor.bam --input_file:normal /home/xxzhang/workplace/output/normal.bam -vcf ./output_RNA/mutect.vcf --out ./output_RNA/mutect.out

     

    INFO 14:07:23,878 HelpFormatter - --------------------------------------------------------------------------------
    INFO 14:07:23,931 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-0-g72492bb, Compiled 2015/01/21 17:10:56
    INFO 14:07:23,931 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 14:07:23,931 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 14:07:23,934 HelpFormatter - Program Args: --analysis_type MuTect --reference_sequence ./geneome/hg19/hg19.fa --dbsnp ./geneome/hg19/hg19.fa_resource/dbsnp.hg19.vcf --cosmic ./geneome/hg19/hg19.fa_resource/CosmicCodingMuts.hg19.vcf --input_file:tumor /home/xxzhang/workplace/output/tumor.bam --input_file:normal /home/xxzhang/workplace/output/normal.bam -vcf ./output_RNA/mutect.vcf --out ./output_RNA/mutect.out
    INFO 14:07:24,004 HelpFormatter - Executing as xxzhang@mu02 on Linux 3.10.0-862.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_80-b15.
    INFO 14:07:24,004 HelpFormatter - Date/Time: 2021/06/29 14:07:23
    INFO 14:07:24,004 HelpFormatter - --------------------------------------------------------------------------------
    INFO 14:07:24,005 HelpFormatter - --------------------------------------------------------------------------------
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version 3.1-0-g72492bb):
    ##### ERROR
    ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
    ##### ERROR The error message below tells you what is the problem.
    ##### ERROR
    ##### ERROR If the problem is an invalid argument, please check the online documentation guide
    ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ##### ERROR
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ##### ERROR
    ##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
    ##### ERROR Name FeatureType Documentation
    ##### ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
    ##### ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
    ##### ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
    ##### ERROR ------------------------------------------------------------------------------------------

    Maybe isn't the version problem?What is meaning of the error "Please add an explicit type tag :NAME listing the correct type from among the supported types" that means?

    I really feel confused!Because the mutect1 is mainly specialized in the SNV calling while the mutect2 is both used in the SNV and CNV calling and sometimes performed unstablly in some paper's comparison,I prefer to use the mutect1 for somatic calling!

    Thanks s lot!

     

     

     

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    Genevieve Brandt (she/her)

    Unfortunately we only provide support for Mutect2 so we cannot look into this further unless you upgrade. 

    You can look through our legacy forum for Mutect1 information if you wish: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/

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