Parameters

On the "Parameters" tab, you can view and change the sample analysis parameters.

The parameters are divided into three main groups according to which analysis modules these parameters are responsible for:

1. Quality Control
2. Alignment
3. Variant Discovery

Changing Analysis Parameters

To change the threshold value of quality control or alignment metric, or of hard-filtering or copy number variations discovery parameter, click on the current value and edit. To save changes, press Enter or click outside edit value container.

To change the selection of the alignment tool, sequencing type, capture kit features, panel of normals or reference samples panel, click on the value of the corresponding field and select the required option:

To disable or enable the analysis module or its parameter, turn off or turn on, respectively, the corresponding toggle. When the toggle switch is on, it is blue and shifted to the right: , and when it is off, it is gray and shifted to the left:

Applying Analysis Parameter Changes

As soon as you start making changes to the analysis settings, the following notification will appear:

It is not necessary to confirm the changes right away, you can do this when you have finished making all the necessary changes to the analysis settings by clicking on .

info

Applying parameter changes will restart the sample analysis process from the step that was changed. For example, if you change the threshold of the hard-filtering parameter, the Germline SNVs/Indels discovery pipeline will restart from the filtering stage.

caution

If you disable one of the analysis modules, you will lose all its progress, so if you want to turn it back on, the process will start from the beginning.

info

By changing the parameters for one sample from a set (for example, for a tumor sample from a tumor/normal sample set), you change the parameters for all samples from the set.

To cancel the changes made, click on or just leave the page - the changes will not be saved.

tip

If you plan to frequently use the same parameters to analyze multiple samples, then instead of changing the settings on the sample parameters tab each time, it is convenient to create a settings preset that can be applied to samples during sample set adding. You can read about how to do this here.