Update README.md

README.md

@@ -5,11 +5,11 @@ Mutation-Server is a Java library to detect heteroplasmic and homoplasmic sites
 It has been integrated in [mtDNA-Server](https://mtdna-server.uibk.ac.at). For scalability, Mutation-Server is parallelized using Hadoop MapReduce but also available as a standalone tool.
 
 ## Standalone Usage
-You can run Mutation-Server as a standalone tool starting with BAM files and detecting heteroplasmic and homoplasmic sites.
+You can run Mutation-Server as a standalone tool starting with BAM files and detecting heteroplasmic and homoplasmic sites. By default BAQ is set (``--noBaq`` otherwise) and no indels (beta feature, ``--indel`` otherwise) are called.
 ```
-wget https://github.com/seppinho/mutation-server/releases/download/v1.1.8/mutation-server-1.1.8.jar
+wget https://github.com/seppinho/mutation-server/releases/download/v1.1.9/mutation-server-1.1.9.jar
 
-java -jar mutation-server-1.1.8.jar  analyse-local --input <file/folder> --output <file> --reference <fasta> --level 0.01
+java -jar mutation-server-1.1.9.jar  analyse-local --input <file/folder> --output <file> --reference <fasta> --level 0.01
 ```
 
 ## Output Format