Meaning of _MIXED and _UNAVAILABLE fields

gene

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

Geraldine_VdAuwera

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.

gene

Thank you.