Filter on Custom Criteria

The Filter on Custom Criteria tool can be used to identify and extract variants, annotations, or features that fulfill certain criteria. It will create a filtered copy of the input containing only the items that were not filtered away.

To run the Filter on Custom Criteria tool, go to:

        Toolbox | Utility Tools (Image utilities_closed_16_n_p) | Filter on Custom Criteria (Image filter_on_custom_feature_16_n_p)

In the first step, select an input to be filtered. This can be a variant track (Image variant_track_16_n_p), annotation track (Image annotation_track_16_n_p), expression track (Image rnaseqtrack_16_h_p), statistical comparison track (Image stats_track_16_n_p), statistical comparison table (Image stats_table_16_n_p), miRNA seeds table (Image rna_seeds_table_16_n_p), IsomiR table (Image isomir_count_table_16_n_p) among others. Click Next.

In the Filter criteria dialog, use the browse icon (Image browse) to select an element that contains at least all the criteria on which you want to filter the input. Once specified, click the Load Annotations button to create the drop down menu available in the filter field below. The drop down menu is constructed from the table view of the selected element.

An example of filter criteria is shown in figure 35.7. In this example, all variants that are not found on chromosome 1 and that are not homozygous are filtered away. As a result only variants that are homozygous and found on chromosome 1 are kept. The bottom filter field on the figure shows the various other filter criteria available after pressing the Load Annotations button.

Image filter_on_custom_criteria
Figure 35.7: Create filter criteria to extract the variants of interest. In this example, the tool is configured to extract the homozygous variants found on chromosome 1.

The output from the Filter on Custom Criteria tool is a copy of the input containing only the items that satisfy the specified filter criteria.