HaplotypeCaller and VariantRecalibrator with QUEUE

userNameuserName Posts: 11Member

Hi team,
I have a basic question, sorry. I am trying to use HaplotypeCaller and VariantRecalibrator with QUEUE but I don't know how add:

VariantRecalibrator.mode = BOTH

HaplotypeCaller.genotyping_mode = DISCOVERY

I get a "not found: value BOTH/DISCOVERY" error.

Thank you in advance,

Comments

  • userNameuserName Posts: 11Member

    Ok, I think:

    VariantRecalibrator.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.BOTH

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,187Administrator, GATK Dev admin

    You can use that, or specify the values as strings, e.g. "BOTH" instead of BOTH

    Geraldine Van der Auwera, PhD

  • userNameuserName Posts: 11Member
    edited October 2013

    Thank you, Geraldine. If I try with:

    VariantRecalibrator.mode ="BOTH"


    I get this:

    ERROR 05:38:54,770 QScriptManager - type mismatch;
    found : java.lang.String("BOTH")
    required: org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode
    ERROR 05:38:54,773 QScriptManager - VariantRecalibrator.mode = "BOTH"

    Post edited by userName on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,187Administrator, GATK Dev admin

    Ah, my mistake then. You were right the first time :)

    Geraldine Van der Auwera, PhD

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