update with filtering vignette

filtering.qmd

@@ -0,0 +1,62 @@
+---
+title: "Filtering"
+format: html
+---
+
+# Why Filter?
+
+Filtering your annotated variants lets you query interesting subsets of your variants. 
+
+A secondary purpose of filtering is when you want to view your results in the results viewer and you have more than 100K variants. 
+
+# Filtering Roadmap
+
+
+```{mermaid}
+A["Results Viewer"] --> B
+B["Build Filter in GUI"] --> C["Save JSON filter"]
+C --> D["Apply filter to New Set"]
+C --> E["Apply Filter on CLI"]
+```
+
+# Filtering in the GUI
+
+Once you have your annotated results, you can filter variants in the results viewer. There are 4 kinds of filters:
+
+- Samples
+- Genes
+- Sample Properties
+- Variant Properties
+
+We will go through each of these filters and their functionality.
+
+## Samples
+
+You can remove variants associated with a set of sample IDs by unselecting them in the checkboxes here.
+
+## Genes
+
+Gene-level filtering can be done here. You can dinput a list of genes, separated by line-breaks 
+
+## Sample Properties
+
+## Variant Properties
+
+
+# Boolean Operations
+
+You can build more sophisticated operations by combining each filter step using Boolean logic.
+
+By default, the filters are combined using **AND** logic, which are more restrictive. For example ... 
+
+These filters can also be combined using **OR** logic, which is more permissive (that is, these filters will return a greater number than the **AND** logic) we might want variants that ...
+
+
+# Exporting Filters
+
+Filters can be exported and saved as JSON files for further reuse. 
+
+
+# Applying filters on the command line
+
+JSON filters can also be applied on the command-line