Filter annotations on name

The name filter allows you to input a list of names to create a new track only with these names. This is useful if you wish to filter your variants so that only those within certain genes are reported. The proposed workflow would be to first create a new gene track only containing the genes of interest. This is done using this tool. Next, use the filter from overlapping annotations tool (see Filter against overlapping annotations) to filter the variants based on the track with genes of interest.

        Toolbox | Track Tools (Image track_tools) | Annotate and Filter | Filter Annotations on Name

Select the track you want to filter and click Next.

Image filter_on_names_step2
Figure 24.11: Specify names for filtering.

As shown in figure 24.11, you can specify a list of names of annotations. Each name should be on its own line.

At the bottom you can choose whether you want to keep the annotations that are found, or whether you wish to exclude them. In the use case described above, you would want to make a track, only keeping the annotations that match the names. Sometimes the other option can be useful, for example if you wish to screen certain categories of genes from the analysis (for example excluding all cancer genes to reduce the risk of coincidental findings when analyzing patient samples).