diff --git a/README.md b/README.md
index 50337cb..7703076 100644
--- a/README.md
+++ b/README.md
@@ -120,6 +120,10 @@ Example: `--cnvcallers purple`
 `--svcallers`- - Comma separated argument for selecting only specified SV vallers. Adding flag allows only certain callers to run.  
 Example: `--svcallers gridss`
 
+`--ffpe`- - Adds additional filtering for FFPE by detecting strand orientation bias using SOBDetector. 
+
+`--exome`- - Limits calling to intervals provided in target bed to reduce time and to account for exome sequencing specific parameters.
+
 ## Running LOGAN
 Example of Tumor_Normal calling mode 
 ```bash
diff --git a/docs/user-guide/pipeline.md b/docs/user-guide/pipeline.md
index 39ce834..174905b 100644
--- a/docs/user-guide/pipeline.md
+++ b/docs/user-guide/pipeline.md
@@ -100,6 +100,10 @@ Example: `--cnvcallers purple`
 `--svcallers`- - Comma separated argument for selecting only specified SV vallers. Adding flag allows only certain callers to run.  
 Example: `--svcallers gridss`
 
+`--ffpe`- - Adds additional filtering for FFPE by detecting strand orientation bias using SOBDetector. 
+
+`--exome`- - Limits calling to intervals provided in target bed to reduce time and to account for exome sequencing specific parameters.
+
 ## Running LOGAN
 Example of Tumor_Normal calling mode 
 ```bash