GATK4 Variant Recalibrator not recognizing format of --truth-sensitivity-tranche argument

breardonbreardon Cambridge, MAMember, Broadie
edited February 21 in Ask the GATK team

The following error is observed when running VariantRecalibrator with the --truth-sensitivity-tranche argument.

A USER ERROR has occurred: Argument truth-sensitivity-tranche has a bad value: [100.0,. Problem constructing Double from the string '[100.0,'.

My run statement is

./gatk VariantRecalibrator --reference $reference --variant $VCF --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /path/hapmap_3.3.b37.vcf --resource:omni,known=false,training=true,truth=true,prior=12.0 /path/1000G_omni2.5.b37.vcf --resource:1000G,known=false,training=true,truth=false,prior=10.0 /path/1000G_phase1.snps.high_confidence.b37.vcf --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /path/dbsnp_138.b37.vcf --use-annotation QD --use-annotation MQRankSum --use-annotation ReadPosRankSum --use-annotation FS --use-annotation MQ --use-annotation InbreedingCoeff --mode SNP --truth-sensitivity-tranche [100.0, 99.9, 99.0, 90.0] --output ${prefix}.SNP.recal --tranches-file ${prefix}.SNP.tranches --rscript-file ${prefix}.SNP.R

This error has been reproducible with both the local downloaded executable of GATK4 and the docker image, broadinstitute/gatk:latest. The argument was also passed exactly as listed on the formal documentation page for Variant Recalibrator.

--truth-sensitivity-tranche, -tranche [100.0, 99.9, 99.0, 90.0]
The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent).

Issue · Github
by Sheila

Issue Number
2967
State
open
Last Updated

Best Answer

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    Accepted Answer

    @breardon
    Hi,

    I have a feeling the documentation is misleading. Can you try --truth-sensitivity-tranche 100.0 --truth-sensitivity-tranche 99.9 --truth-sensitivity-tranche 99.0 --truth-sensitivity-tranche 90.0? Let us know if that works, and I can see if we can make the documentation more clear.

    -Sheila

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    Accepted Answer

    @breardon
    Hi,

    I have a feeling the documentation is misleading. Can you try --truth-sensitivity-tranche 100.0 --truth-sensitivity-tranche 99.9 --truth-sensitivity-tranche 99.0 --truth-sensitivity-tranche 90.0? Let us know if that works, and I can see if we can make the documentation more clear.

    -Sheila

  • breardonbreardon Cambridge, MAMember, Broadie

    Ah, that was silly of me. That worked! Thank you Sheila!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @breardon
    Hi,

    I remember another user being confused about that a while back and we never changed the docs since the team thought the docs were clear enough. However, I will bring this up again and see if we can add an example in the command.

    -Sheila

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