How to create a custom sample analysis workflow

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

Click on the Add custom panel button to configure the new panel (figure 13.8).

Image configurecustomguide
Figure 13.8: 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 analysis. Choose the application for the analysis. It is also possible to use a pre-existing analysis as a template by selecting it from the drop down menu. In that case, the name of the analysis chosen in the drop-down menu will fill the "Analysis 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 Analysis 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 Variant 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 launching workflows via the Analyze QIAGEN Samples guide, but can be when running workflows from the Toolbox.

Variants failing to meet the thresholds for the following would not be included in the filtered output:

Once your custom analysis is configured, click Save to add the custom workflow to the list of workflows available from the Analyze QIAseq Samples 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 sample analysis).