.. _getting_started_with_preview_columns: Getting Started with Preview Columns #################################### Configure genotype columns in Genotype Browser +++++++++++++++++++++++++++++++++++++++++++++++ Once you have annotated your variants, the additional attributes produced by the annotation can be displayed in the variants preview table. In our example, the annotation produces three additional attributes: * ``gnomad_v4_genome_ALL_af`` * ``CLNSIG`` * ``CLNDN`` Let us add these attributes to the variants preview table for the ``example_dataset`` dataset. In the preview table, each column could show multiple values. In GPF, when you want to show multiple values in a single column, you need to define a **column group**. The **column group** is a collection of attributes that are shown together in the preview table. The values in a column group are shown in a single cell. By default, the study configuration includes several predefined column groups: ``family``, ``variant``, ``genotype``, ``effect`` and ``frequency``. .. figure:: getting_started_files/example-dataset-default-column-groups.png Default column groups in the `Preview Table` In the study configuration, you can define new column groups or redefine already existing ones. Let us redefine the existing column group ``frequency`` to include the gnomAD frequency and define a new column group ``clinvar`` to include the ClinVar attributes. The column group is defined in the ``column_groups`` section of the configuration file. Edit the ``example_dataset.yaml`` dataset configuration in ``minimal_instance/datasets/example_dataset`` and add the following section at the end of the configuration file: .. code-block:: yaml :linenos: genotype_browser: column_groups: frequency: name: frequency columns: - allele_freq - gnomad_v4_genome_ALL_af clinvar: name: ClinVar columns: - CLNSIG - CLNDN preview_columns_ext: - clinvar In lines 3-7, we re-define the existing column group ``frequency`` to include the study frequency ``allele_freq`` and gnomAD frequency ``gnomad_v4_genome_ALL_af``. In lines 9-13, we define a new column group ``clinvar`` that contains the values of the annotation attributes ``CLNSIG`` and ``CLNDN``. In lines 15-16, we extend the preview table columns. The new column groups ``clinvar`` will be added to the preview table. If we now stop the ``wgpf`` tool and rerun it, we will be able to see the new columns in the preview table. From the GPF instance `Home Page`, follow the link to the `Example Dataset` page and choose the `Genotype Browser`. Select all checkboxes in `Present in Child`, `Present in Parent` and `Effect Types` sections. .. image:: getting_started_files/example-dataset-genotype-browser-extended-columns-filters.png Then click the `Preview` button and will be able to see all the imported variants with their additional attributes coming from the annotation. .. figure:: getting_started_files/example-dataset-genotype-browser-extended-columns-variants.png Example Dataset genotype browser displaying variants with additional columns `gnomAD v4` and `ClinVar`. Configure phenotype columns in Genotype Browser +++++++++++++++++++++++++++++++++++++++++++++++ The Genotype Browser allows you to add phenotype attributes to the table preview and the download file. Phenotype attributes show values from a phenotype database that are associated with the displayed family variant. To configure such a column, you need to specify the following properties: * ``source`` - the measure ID whose values will be shown in the column; * ``role`` - the role of the person in the family for which we are going to show the phenotype measure value; * ``name`` - the display name of the column in the table. Let's add some phenotype columns to the `Genotype Browser` preview table in `Example Dataset`. To do this, you need to define them in the study's config, in the genotype browser section of the configuration file. We are going to modify the ``example_dataset.yaml`` dataset configuration in ``minimal_instance/datasets/example_dataset/example_dataset.yaml``: .. code-block:: yaml :linenos: :emphasize-lines: 2-12,27-31,35 genotype_browser: columns: phenotype: prb_verbal_iq: role: prb name: Verbal IQ source: iq.verbal_iq prb_non_verbal_iq: role: prb name: Non-Verbal IQ source: iq.non_verbal_iq column_groups: frequency: name: frequency columns: - allele_freq - gnomad_v4_genome_ALL_af clinvar: name: ClinVar columns: - CLNSIG - CLNDN proband_iq: name: Proband IQ columns: - prb_verbal_iq - prb_non_verbal_iq preview_columns_ext: - clinvar - proband_iq Lines 2-12 define the two new columns with values coming from the phenotype data attributes: * ``prb_verbal_iq`` - is a column that uses the value of the phenotype measure ``iq.verbal_iq`` for the family proband. The display name of the column will be `Verbal IQ`; * ``prb_non_verbal_iq`` - is a column that uses the value of the phenotype measure ``iq.non_verbal_iq`` for the family proband. The display name of the column will be `Non-Verbal IQ`. We want these two columns to be shown together in the preview table. To do this, we need to define a new **column group**. In lines 27-31, we define a column group called ``proband_iq`` that contains the columns ``prb_verbal_iq`` and ``prb_non_verbal_iq``. To add the new column group ``proband_iq`` to the preview table, we need to add it to the ``preview_columns_ext`` section of the configuration file. In line 35, we add the new column group ``proband_iq`` at the end of the preview table. When you restart the server, go to the `Genotype Browser` tab of the ``Example Dataset`` dataset and select all checkboxes in `Present in Child`, `Present in Parent` and `Effect Types` sections: .. image:: getting_started_files/example-dataset-proband-iq-column-group-filters.png When you click on the `Table Preview` button, you will be able to see the new column group ``proband_iq`` in the preview table. .. figure:: getting_started_files/example-dataset-proband-iq-column-group-variants.png Example Dataset genotype browser using pheno measures columns .. note:: For more on study configuration, see the :doc:`study_configuration` section.