Merge branch 'master' into feat/custom_alignment_props

config/README.md

@@ -36,6 +36,7 @@ Missing values can be specified by empty columns or by writing `NA`. Lines can b
 Varlociraptor supports integrated uncertainty aware calling and filtering of variants for arbitrary scenarios. These are defined as so-called scenarios, via a [variant calling grammar](https://varlociraptor.github.io/docs/calling#generic-variant-calling).
 * For each group, a scenario is rendered via [YTE](https://yte-template-engine.github.io).
 * Therefore, edit the template scenario (`scenario.yaml`) according to your needs. The sample sheet is available for YTE rendering as a pandas data frame in the variable `samples`. This allows to customize the scenario according to the contents of the sample sheet. You can therefore add additional columns to the sample sheet (e.g. purity) and access them in the scenario template, in order to pass the information to Varlociraptor.
+* Example scenarios for various use cases can be found in the [scenario catalog](https://varlociraptor.github.io/varlociraptor-scenarios).
 
 # Primer trimming
 

config/config.yaml

@@ -153,7 +153,9 @@ calling:
       expression: "ANN['SYMBOL'] in AUX['super_interesting_genes']"
   fdr-control:
     threshold: 0.05
-    # denote FDR control mode, see https://varlociraptor.github.io/docs/filtering
+    # Denote FDR control mode.
+    # The default (local-smart) is recommended because it provides the most realistic and intuitive results.
+    # See see https://varlociraptor.github.io/docs/filtering for details.
     mode: local-smart
     events:
       # Add any number of events here to filter for.