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.

administration/getting_started/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:

 1genotype_browser:
 2  column_groups:
 3    frequency:
 4      name: frequency
 5      columns:
 6      - allele_freq
 7      - gnomad_v4_genome_ALL_af
 8
 9    clinvar:
10      name: ClinVar
11      columns:
12      - CLNSIG
13      - CLNDN
14
15  preview_columns_ext:
16    - 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.

administration/getting_started/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.

administration/getting_started/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:

 1genotype_browser:
 2  columns:
 3    phenotype:
 4      prb_verbal_iq:
 5        role: prb
 6        name: Verbal IQ
 7        source: iq.verbal_iq
 8
 9      prb_non_verbal_iq:
10        role: prb
11        name: Non-Verbal IQ
12        source: iq.non_verbal_iq
13
14  column_groups:
15    frequency:
16      name: frequency
17      columns:
18      - allele_freq
19      - gnomad_v4_genome_ALL_af
20
21    clinvar:
22      name: ClinVar
23      columns:
24      - CLNSIG
25      - CLNDN
26
27    proband_iq:
28      name: Proband IQ
29      columns:
30      - prb_verbal_iq
31      - prb_non_verbal_iq
32
33  preview_columns_ext:
34    - clinvar
35    - 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:

administration/getting_started/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.

administration/getting_started/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 study_configuration section.