GATK4 VariantAnnotator


Has this tools been removed in the last release ? :o


Best Answer


  • Hi Sheila,

    I used gatk4 for variant annotation of my vcf file with dbsnp with the below command:

    Gatk VariantAnnotator –R genom.fa –I file1.bam –V file1.vcf –A coverage –D All_20180418.vcf

    GATK4 said “Warning: VariantAnnotator is a BETA tool and is not yet ready for use in production” and didn’t return me any output. Could you please help me out what's wrong? I'm not sure about the -I flag in my above command, please kindly tell me if it is correct?


  • bhanuGandhambhanuGandham Member, Broadie, Moderator

    Hi Ana_22,

    Required Arguments:

    --output,-O:File The file to which variants should be written Required.

    --variant,-V:String A VCF file containing variants Required.

    Please provide an output file. That should solve the problem.
    I hope that helps. :)


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