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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

There are 2 comments on this article. To see them or add your own, view this post on the forum