diff --git a/README.md b/README.md
index f49a651..8b173c9 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # SV conflict workflow
 
-### Filetree
+## Filetree
 The project is built up similarly to other snakemake workflows.
 
 Root
@@ -9,7 +9,7 @@ Root
 - results
 - workflow
 
-#### Config
+### Config
 The [`config.yaml`](config/config.yaml) contains global configurations for running the
 pipeline. Currently, the following settings can be made:
 
@@ -34,10 +34,10 @@ pw_alignment:
 specifying string (like chr12:456-876).
 
 
-#### Resources
+### Resources
 Here you have to put all the resources that snakemake is going to use.
 
-##### Resources
+#### Resources
 In the `references` directory, you should put the fasta files + indexes for
 each reference that you want to use. Also, `references/liftover` should
 include a file called `liftover_config.json` which defines the liftover
@@ -67,7 +67,7 @@ where `liftover_config.json` looks like:
 }
 ```
 
-##### Samples
+#### Samples
 The `samples` subdirectory should contain a folder for each sample that
 is going to be used in the workflow.
 Each sample's folder again includes a folder for each reference, where
@@ -91,7 +91,7 @@ samples/
                 regions.txt
 ```
 
-#### Results
+### Results
 The results directory will include all results after the workflow has
 run. The structure will look like the following:
 ```