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  • VariantAnnotator ReadPositionRankSumTest Error

    my command:
    java -Xmx20g -jar GenomeAnalysisTK-1.3-24-gc8b1c92/GenomeAnalysisTK.jar \
    -T VariantAnnotator \
    -R hg19fastadatabase/ucsc.hg19.fasta \
    -I dedup_mate_recal.bam \
    --variant recal_raw.vcf \
    --dbsnp hg19_GATK1_1/dbsnp_132.hg19.vcf \
    -o output2.vcf \
    -A FisherStrand \
    -A MappingQualityRankSumTest \
    -A ReadPositionRankSumTest \
    -A RMSMappingQuality \
    -A MappingQualityZero \
    -A QualByDepth \
    -A HaplotypeScore \
    -A DepthOfCoverage \
    -A BaseQualityRankSumTest

    I got the Error:
    ##### ERROR MESSAGE: Invalid command line: Argument annotation has a bad value: Class ReadPositionRankSumTest is not found; please check that you have specified the class name correctly
    ##### ERROR ------------------------------------------------------------------------------------------



    ReadPositionRankSumTest (ReadPosRankSum)

    how can i solve this problem

  • #2
    Hi there,

    the correct name of the annotation is ReadPosRankSumTest.
    Version GATK-1.2-4

    Cheers,
    msa

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