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error in Mutect2 when using dbsnp?

etcetc Member
edited February 2018 in Ask the GATK team

I am running Mutect2 with various options. Most options are running as expected, but when using the --dbsnp version I am now seeing an error:
A USER ERROR has occurred: dbsnp is not a recognized option

In the resulting error log, --dbsnp does not appear among the list of recognized arguments. In the online tool documentation, however, it is listed as a valid option (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php#--dbsnp)
I am using the GATK docker image with GATK version

gatk-4.beta.5 (local) jar accepts the --dbsnp option as valid.
Please advise.

Best Answer


  • BegaliBegali GermanyMember ✭✭
    edited August 2018

    Hi @shlee

    I am trying to use
    /Downloads/gatk- --java-options "-Xmx2g" Mutect2 -R hg38.fa -I recal109_17.bam -tumor 109_17 --germline_resource somatic-hg38_af-only-gnomad.hg38.vcf.gz --normal_panel somatic-hg38_1000g_pon.hg38.vcf.gz -L intervals.list -O tumor_unmatched_m2_snvs_indels109_17java.vcf

    it provides me also the same error even if I am using GATK4 Mutect2
    A USER ERROR has occurred: germline_resource is not a recognized option

    thanks in advance

    Post edited by Begali on
  • BegaliBegali GermanyMember ✭✭

    Hi @shlee
    I fix it was my mistak it is --germline-resource not --germline_resource
    -pon not --normal_panel
    resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list not intervals.list


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