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I cannot find the issue here for this VariantFiltration error

~/gatk-4.0.8.1/gatk VariantFiltration -R Refgenome.fasta -V KMM2_raw_snps_indels_annotations_09302018.vcf -filter "QD < 2.0 || FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20. || InbreedingCoeff < -0.8" --filter-name "indelfilter1" -O KMM2_filtered_indels_indelfilter1_10012018.vcf

Runtime.totalMemory()=2281701376
java.lang.IllegalArgumentException: Argument indelfilter1has a bad value. Invalid expression used (QD < 2.0 || FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20. || InbreedingCoeff < -0.8). Please see the JEXL docs for correct syntax.
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:283)
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:243)
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:259)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.onTraversalStart

Best Answers

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    Accepted Answer

    Hi @kmmahan

    The error is due to incorrect syntax. You have used "--filter" argument instead of "--filter-expression". Please change that and try again. Hope this helps.

    Regards
    Bhanu

  • kmmahankmmahan Member
    edited October 2018

    ugh- it didn't work

  • kmmahankmmahan Member
    edited October 2018

    I changed it and still got the same error - and also the help section says you can use -filter or --filter-expression.

    ~/gatk-4.0.8.1/gatk VariantFiltration -R Reference_genome.fasta -V KMM2_raw_snps_indels_annotations_09302018.vcf --filter-expression "QD < 2.0 || FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20. || InbreedingCoeff < -0.8" --filter-name "indelfilter" -O KMM2_filtered_indels_indelfilter1_10012018.vcf

    IllegalArgumentException: Argument indelfilterhas a bad value. Invalid expression used (QD < 2.0 || FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20. || InbreedingCoeff < -0.8). Please see the JEXL docs for correct syntax.
    at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:283)
    at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:243)
    at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:259)
    at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.onTraversalStart(VariantFiltration.java:283)

  • kmmahankmmahan Member

    It's something with --filter-name "indelfilter"

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