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  • angieant
    Junior Member
    • Nov 2012
    • 1

    #1

    Help: error while running VariantRecalibrator

    experiment: target enrichment and sequencing using Illumina platform

    raw VCF file from UnifiedGenotyper -> Variantrecalibrator

    i got the following error, any potential explanation? Thanks

    "
    ##### ERROR MESSAGE: Bad input: Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadV ariants arugment but this is unsafe.
    "

    script used:

    java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -T \
    -mode BOTH -nt 4 \
    -R hg19_all_MT.fasta \
    -input two.final.vcf \
    -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.fy_left.vcf \
    -resourcemni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.site.fy.vcf \
    -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp137_sort_fy_left.vcf \
    -recalFile two.final.vcf.reca \
    -tranchesFile two.final.vcf.tranches \
    -rscriptFile two.final.vcf.R \
    -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -tranche 85.0 -tranche 80.0 \
    -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ -an FS -an HRun

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