4. Project WorkflowΒΆ

This tutorial was accompanied by a VarSeq project contained in a ZIP file. Before starting, download the ZIP file, and extract the contents to a convenient location. Then open up the project, AMP Tutorial Example, by double clicking on the file.

This is a premade project where variants have been imported, a filter chain composed, and biomarkers selected. Upon first opening the project, you can see a filter chain on the left and larger variant table on the right. Looking to the upper right-hand corner will show the summation of this project which contains data from 4 samples and a total of 126,966 variants.

new project introduction

Figure 4-1: A new project introduction in VarSeq.

Closer examination of the filter chain shows the following filters were selected:
  • Filter field = PASS
  • Genotype Quality >= 90
  • Read Depth >= 200
  • Variant Allele Frequency < 0.1
  • Effect is LoF or Missense OR 2+ out of 4 predicted splicing disruptive
  • Is in the COSMIC database
  • Classified by the ACMG Classifier as Pathogenic.

Overall, this filter chain is used to first reduce the large amount of variants down to higher quality variants, then variants that look to be causing problems like LoF or splice disrupting. And finally, variants are filtered to those that are present in the COSMIC are classified to be Pathogenic. For the sample displayed on opening, this reduces the pool of variants from over 100,000 to 4 candidates.

Note

These filters where chosen to provide interesting examples in our final filter list and not as an example production filtering workflow. For example, you most likely want to include all VUS and Likely Pathogenic variants in the Classification filter.

varseq project variant table

Figure 4-2: The VarSeq project with filter chain and variant table.

Once we have determined a smaller selection of variants to explore further, we will open up the AMP Guidelines. This is done by selecting the plus sign next to the Variants tab and selecting VSClinical.

open AMP guidelines

Figure 4-3: Opening the VSClinical AMP Guidelines.

From the drop-down menu on this new VSClinical tab, select AMP Guidelines.

The first dialog that appears on the new tab is the VSClinical Dependencies Download dialog. This dialog is split into 3 sections: Required to Download, Recommended to Download, and Optional Downloads. It is common practice to select the Required and Recommended downloads as the Optional Downloads are larger files and are mainly only downloaded for users performing offline analyses.

download dependencies

Figure 4-4: The VSClinical Dependencies Download dialog.

It should also be noted that users may have previous versions of dependencies already saved. If so, a note in blue will show up describing what the previous version is and then the dependency will be checked to allow the user to download the current version. Make your download selection and select the Download button. Download progress will be displayed and once complete, select Continue.

The next dialog to appear will be asking the user to define an assessment catalog for the Internal Database of Cancer Interpretations: and an assessment catalog for the Internal Database of Classified Germline ACMG Variants:. If assessment catalogs for either category already exist, they can be found or navigated to from the corresponding drop-down menu, but we want to create new assessment catalogs for this tutorial by selecting Create Catalog first for the Internal Database of Cancer Interpretations section.

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.

assessment catalog creation

Figure 4-5: Creating an assessment catalog.

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.

Repeat this step for the Internal Database of Classified Germline ACMG Variants: section. The example below shows 2 created SQLite assessment catalogs called Somatic AC and Germline AC.

assessment catalog selection

Figure 4-6: Filling assessment catalog selections.

As one last step before we explore the AMP Guidelines, we will stash the filter chain by hovering the mouse over the upper left-hand corner of the filter chain tab and click on the arrow icon that appears.

stash filter chain

Figure 4-: Stash filter chain with arrow.