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  • error_Values for InbreedingCoeff annotation not detected for ANY training variant in

    Hi all, when I run GATK VariantRecalibrator using the following commands: run_gatk.sh
    -T VariantRecalibrator
    -R GRCh37/human_g1k_v37.fasta -input raw4.snp.vcf
    -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf
    -resourcemni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf
    -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_134.b37.vcf
    -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff
    -mode SNP
    -recalFile raw4.snp.vcf.recal
    -tranchesFile raw4.snp.vcf.tranches -rscriptFile raw4.snp.vcf.plots.R"

    error message as follows:

    ERROR ------------------------------------------------------------------------------------------

    ERROR A USER ERROR has occurred (version 2.0-39-gd091f72):

    ERROR The invalid arguments or inputs must be corrected before the GATK can proceed

    ERROR Please do not post this error to the GATK forum

    ERROR

    ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.

    ERROR Visit our website and forum for extensive documentation and answers to

    ERROR commonly asked questions http://www.broadinstitute.org/gatk

    ERROR

    ERROR MESSAGE: Bad input: Values for InbreedingCoeff annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wi...riantAnnotator

    Which kind of annotations should I add and how? I'm quite worry, thanks a lot!

  • #2
    I removed "-an InbreedingCoeff" and added --maxGaussians 4 , problem resolved
    don't know if that's good

    Comment

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