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Variant Recalibrator Error

Hello everyone,

I am using the VariantRecalibrator tool in the following command:

"
export Gold="/ibex/scratch/alsaedsb/Task_w1/ref/Mills_and_1000G_gold_standard.indels.b37.vcf"
export dbsnp="/ibex/scratch/alsaedsb/Task_w1/ref/dbsnp_138.b37.vcf"

gatk VariantRecalibrator -V $VCF/${PREFIX}_SNP_INDLS_only_VCF.vcf -O $RECAL/${PREFIX}_INDEL_HG.recal --tranches-file $RECAL/${PREFIX}_INDEL_HG.tranche --trust-all-polymorphic -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode INDEL --max-gaussians 4 --resource:mills,known=false,training=true,truth=true,prior=12 ${Gold} --resource:dbsnp,known=false,training=true,truth=true,prior=2.0 ${dbsnp}"

and have submitted the script on slurm and I got the following error:

"A USER ERROR has occurred: The argument: "resource/resource" does not accept tags: "Mills,known=false,training=true,truth=true,prior=12""


I have tried many ways to solve that , but the error is there, May any one help me to solve it ?
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Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @Sakhaa

    Which version of GATK are you using?

  • SakhaaSakhaa Member
  • SakhaaSakhaa Member
    Hi @bhanuGandham
    I am using : gatk 4.1.2.0
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Sakhaa

    Can you please post the entire error log.

  • SakhaaSakhaa Member
    edited August 13
    sure @bhanuGandham

    "[VCF]$ gatk VariantRecalibrator -V S_18_2123_NIST-8398_AD008_L008_SNP_INDLS_only_VCF.vcf -O $RECAL/INDEL_HG.recal --tranches-file $RECAL/INDEL_HG.tranche --trust-all-polymorphic -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode INDEL --max-gaussians 4 --resource:Mills,known=false,training=true,truth=true,prior=12 /ibex/scratch/alsaedsb/Task_w1/ref/Mills_and_1000G_gold_standard.indels.b37.vcf --resource:dbsnp,known=false,training=true,truth=true,prior=2.0 ${dbsnp}
    Using GATK jar /sw/csi/gatk/4.0.1.1/el7_binary/bin/gatk-package-4.0.1.1-local.jar
    Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /sw/csi/gatk/4.0.1.1/el7_binary/bin/gatk-package-4.0.1.1-local.jar VariantRecalibrator -V S_18_2123_NIST-8398_AD008_L008_SNP_INDLS_only_VCF.vcf -O /ibex/scratch/alsaedsb/BEST_WF/RECAL/INDEL_HG.recal --tranches-file /ibex/scratch/alsaedsb/BEST_WF/RECAL/INDEL_HG.tranche --trust-all-polymorphic -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode INDEL --max-gaussians 4 --resource:Mills,known=false,training=true,truth=true,prior=12 /ibex/scratch/alsaedsb/Task_w1/ref/Mills_and_1000G_gold_standard.indels.b37.vcf --resource:dbsnp,known=false,training=true,truth=true,prior=2.0 /ibex/scratch/alsaedsb/Task_w1/ref/dbsnp_138.b37.vcf
    USAGE: VariantRecalibrator [arguments]

    Build a recalibration model to score variant quality for filtering purposes
    Version:4.0.1.1"
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
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