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About VariantRecalibration

laportelaporte MontrealMember

From GATK 2.7 to 3.2, we noticed that the FILTER field changed using VariantRecalibration.
Previously, we had the filter names in regards to the model build by the VariantsRacalibration. Now it's either PASS or LOW_VSQLOD

Is there a way to have the ApplyRecalibration walker assign the tranche name as filter, ie
VQSRTrancheINDEL99.00to99.90
VQSRTrancheINDEL99.90to100.00
VQSRTrancheSNP99.00to99.90
VQSRTrancheSNP99.90to100.00

instead of only LOW_VSQLOD ?

Thanks!

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @laporte‌

    Hi,

    I am not sure what you are referring to.

    The filterName column in the output tranches file contains the tranche name (ie VQSRTrancheSNP0.00to90.00).

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi again,

    Please disregard my previous answer. I made a mistake. I will get back to you after confirming with the team.

    Thanks,
    Sheila

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