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Basic Filtering of Variants

Basic filtering columns are at the top of the table:

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On "Profile settings" page, you can configure which filtering mode you will see when you first open the sample SNV Viewer page: Basic or Advanced.

Basic Filters#

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On "Profile settings" page, you can change the choice of basic filters. The following describes in detail those filters that are chosen by default.

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Table filtering is saved when you exit the SNV Viewer page.

1. Origin#

Filtering by mutation type: Somatic, Germline.

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"Origin" filter column is hidden in the Basic Filtering mode of SNV Viewer with germline mutations.

Both here and in all subsequent cases, the filtering algorithm is as follows:

  • Click on the filter field;
  • Select the needed filtering option from the drop-down list, or type the option you are looking for in the search box and select from the found.

Done! Filter applied. The selected filter can be seen in the field (in this case, the "Somatic" origin is selected):

2. Gene panel#

Filtering variants by localization in certain genes from the panel. You can add a gene panel on "Gene Panels" page or import a panel from the Library of the most common clinical panels. To import, click on "Import from Library":

Select the required panels by ticking them in the window that opens:

and click on to add panel.

3. Gene#

Filtering variants by localization in the gene transcript. The transcript is given in brackets next to the official gene name. You can filter variants by several genes at once. To do this, tick the required genes and click outside the value area:

If several transcripts are known for a gene, the list presents all of them:

4. Ontology#

Filter variants by their localization in genes associated with terms from the Human Phenotype Ontology (HPO) and the Mondo Disease Ontology (Mondo). Click the ontology filter field. The search dialog that opens displays the main phenotype groups in a drop-down list:

Methods for searching and selecting a phenotype or disease for filtering:

  • Search directly in the drop-down list. You can navigate the phenotype groups using the and buttons to expand and collapse the list of terms within each group, respectively:

You can also search for a phenotype or disease:

  • by its full or partial name;
  • by its HPO ID (for example, HP:0009733 or 0009733);
  • by its Mondo ID (for example, MONDO:0009733 or 0009733).

For example, searching for "glioma" returns several matching terms:

To select a term for filtering, click the corresponding row. You can filter by either an entire phenotype group or an individual phenotype. After selecting a phenotype (for example, Glioma), its information card is displayed:

The left side of the card displays the full phenotype or disease name with a link to the corresponding page in the HPO or Mondo ontology (provided by the Monarch Initiative), as well as all available information from the selected ontology, including the description, synonyms, comment, and PubMed references.

The center of the card displays the term hierarchy. Parent terms of the selected disease (in this example, Glioma) are shown above it, indicating the phenotype groups to which it belongs. Child terms (phenotypes and diseases that belong to the Glioma group) are displayed below.

The right side of the card contains a list of genes associated with the selected phenotype or disease.

Above the phenotype card, the terms selected for filtering are displayed together with their ontology identifiers. The number of genes associated with each term is shown in parentheses. To open a phenotype card, click the corresponding term. To remove a term from the filter, click the button:

  • Search using the term hierarchy. The phenotype card allows you to navigate through the ontology hierarchy. Click the name of a parent or child phenotype to open its card.
    If the term has not yet been selected for filtering and associated genes are available, click to add it to the variant filter.

  • Search in multi-select mode. Click the right button of the search mode switcher in the upper-left corner of the dialog: . A list of the main phenotype groups with selection checkboxes is displayed.

Search can be performed:

  • by full or partial name;
  • by HPO ID (for example, HP:0009733 or 0009733);
  • by Mondo ID (for example, MONDO:0009733 or 0009733).

For example, searching for "glioma" returns several matching terms:

In multi-select mode, you can select multiple terms simultaneously from the drop-down list. To include a phenotype in the filter, select its corresponding checkbox.

When you have finished selecting phenotypes, click anywhere outside the drop-down list but within the search dialog. The selected filter terms are displayed at the top of the dialog. The number of genes associated with each phenotype is shown in parentheses. Click a phenotype to open its information card. To remove a phenotype, click the button.

To filter variants by genes associated with the selected phenotypes, click . To view the list of selected terms, hover over the ontology filter field:

To clear filtering for all selected terms, hover over the ontology filter field and click the cross icon that appears:

Alternatively, click the ontology filter field and modify the selection in the phenotype search dialog.

5. Min depth level#

Filtering by sequencing depth. You can vary the level using both the plus/minus and the slider. Between 1x and 50x the filter step (scale) is 1, between 50x and 100x is 3, and between 100x and 300x is 7.

6. Saved queries#

Filtering by saved queries is available in two modes:

  • Single query. When a single query is selected, all conditions included in that query are displayed above the table after applying the filter.
  • Multiple queries. When multiple queries are selected, filtering is performed as a logical OR combination of the queries. In this case, only the names of the selected queries are shown above the table, while their conditions can be viewed in the query builder.

Saving queries is described in the corresponding section.

Reset Filtering#

To clear all filters, click on .

To reset a separate filter:

  • Click on the filter field and then on .
  • If the filter allows to select several options at once (for example, filter by Gene), then you can remove one of the selected filter options. To do this, click on the filter field and uncheck the option.
  • To change the selected phenotypes used for variant filtering, click the ontology filter field and modify the selection in the phenotype search dialog. To clear filtering for all selected terms, hover over the ontology filter field and click the cross icon that appears: