4. ACMG Algorithm

This is performed by selecting Add in the title bar and selecting Computed Data…. And under Variant > Per Sample select ACMG Sample Classifier and click OK.

ACMG sample classifier

Figure 4-1: The ACMG Sample Classifier algorithm selection.

Running this algorithm will require some additional annotation sources to be downloaded for use and the status of these sources will be shown in the following dialog.

ACMG classifier dependencies

Figure 4-2: The ACMG Sample Classifier dependencies dialog.

We will keep the default values here, but will associate an existing assessment catalog from the Assessment Catalog drop-down menu if one exists, or create a new catalog if one does not by selecting Create Catalog.

The create catalog will first ask you to determine the database type. The options are SQLite, PostgreSQL, MySQL, or if you have the added feature connected, VSWarehouse.

ACMG assessment catalog selection

Figure 4-3: The ACMG assessment catalog selection.

If not using VSWarehouse, a common choice is using the SQLite type and saving the catalog locally. In either case, select a name or location for the new assessment catalog and select, OK.

At this point an assessment catalog was selected or created and we are ready to run the ACMG Sample Classifier by selecting, OK on this screen as well as on the following screen to keep default values.

This may take a minute to run, but will add the ACMG Sample Classifier results to the variant table.

ACMG classifier results

Figure 4-4: The ACMG Sample Classifier output results.

We will come back to the end of the tutorial to integrate the ACMG Sample Classifier columns into the filter chain. Feel free to review the output, especially the Classification column.

The last step in the algorithm stage is to apply the Genotype Zygosity algorithm. This is accomplished by again selecting Add in the title bar and selecting Computed Data.... From the list of algorithms, select Genotype Zygosity and select OK.

genotype zygosity

Figure 4-6: Adding the Genotype Zygosity algorithm.

The next step is to look at the ACMG Guidelines.