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Meaning of _MIXED and _UNAVAILABLE fields

genegene Posts: 17Member
edited September 2012 in Ask the GATK team

Hi,

I am using VariantEval --evalModule GenotypeConcordance in order to establish concordance and sensitivity metrics against a HapMap reference. In the resulting GATK report I obtain the following fields for a given SNP category (example with HETs):

GenotypeConcordance  CompRod  EvalRod  JexlExpression  Novelty  variable                                value---
GenotypeConcordance  comp     eval     none            all      n_true_HET_called_HET                       6220
GenotypeConcordance  comp     eval     none            all      n_true_HET_called_HOM_REF                      0
GenotypeConcordance  comp     eval     none            all      n_true_HET_called_HOM_VAR                     20
GenotypeConcordance  comp     eval     none            all      n_true_HET_called_MIXED                        0
GenotypeConcordance  comp     eval     none            all      n_true_HET_called_NO_CALL                    318
GenotypeConcordance  comp     eval     none            all      n_true_HET_called_UNAVAILABLE                  0

What is the meaning of the _MIXED and _UNAVAILABLE fields?

Thx,
Gene

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,630Administrator, GATK Developer admin

    Hi Gene,

    n_true_HET_called_MIXED refers to cases where one chromosome was called but not the other (for diploids; more generally, one chromosome not called), resulting in something like ./1. The GATK does not issue such calls (instead a no_call will be issued) but some other programs do.

    n_true_HET_called_UNAVAILABLE is something we use internally for development but it is not relevant for external users like yourself.

    Geraldine Van der Auwera, PhD

  • genegene Posts: 17Member

    Thank you.

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