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VQSR Training

atksatks Member Posts: 16
edited October 2012 in Ask the GATK team

When performing VQSR, the data set has its variants overlapped with the training set, may I know if all the overlapped variants are used in the training or is it down sampled?

Post edited by Geraldine_VdAuwera on

Best Answer

  • rpoplinrpoplin Dev Posts: 122 ✭✭✭
    Accepted Answer

    Hi atks,

    There isn't any downsampling of the training variants however there is some filtering that is done. By looking at the 1D annotation distributions, extreme outliers are removed from the training set. This behavior is controlled with the --stdThreshold argument to VariantRecalibrator.

    I hope that helps,

Answers

  • rpoplinrpoplin Dev Posts: 122 ✭✭✭
    Accepted Answer

    Hi atks,

    There isn't any downsampling of the training variants however there is some filtering that is done. By looking at the 1D annotation distributions, extreme outliers are removed from the training set. This behavior is controlled with the --stdThreshold argument to VariantRecalibrator.

    I hope that helps,

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