How to create a custom panel analysis workflow

For most applications (DNA, RNAscan, RNA, Targeted TMB/MSI, and Targeted Methyl) it is possible to set up a custom workflow.

Click on the Add custom panel button to configure the new panel (figure 2.10).

Image configurecustomguide
Figure 2.10: Configure the workflow with the files corresponding to your custom panel. Here we can see an example where the drop down menu "Copy from" shows all the possible custom Targeted DNA workflows available.

In the General information section, enter the name of the custom panel. Choose the application for the panel. It is also possible to use a pre-existing panel as a template by selecting it from the drop down menu. In that case, the name of the panel chose in the drop-down menu will fill the "Panel name" field, but can also be re-edited for clarity purposes. In the case of Targeted DNA applications, copying an existing panel is the easiest way to set up a workflow in which you have control over the filtering steps.

In the Panel data section, specify the following files (the type of files you have to provide depends on the application):

Targeted DNA custom workflows include filter steps allowing the initial pool of variants found in the data (output in the Unfiltered Variants track) to be reduced to a smaller set of "reliable" variants (output in the Variants passing filters track). The filters are designed especially for the read type and application and are based on the following parameters:

Note that the default values for these parameters are different depending on the sample being analyzed (somatic or germline) and the technology used for sequencing (Illumina or Ion Torrent). They cannot be configured when using the guide, but when running workflows from the Toolbox.

The filters remove variants that are either:

Once your custom panel is configured, click Save to add the custom workflow to the list of workflows available from the Analyze QIAseq Panels guide. Once in the list, a button Edit allows you to change the configuration of the custom workflow. Click Run to follow the instructions given in each dialog (see Start a QIAseq panel analysis).