Merge branch 'master' of https://github.com/seppinho/mutation-server.git

README.md

@@ -5,20 +5,23 @@ 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 CRAM/BAM files and detecting heteroplasmic and homoplasmic sites. By default BAQ is set (``--noBaq`` otherwise) and no indels (beta feature,  ``--indel`` otherwise) are called. Please note that currently only deletions are included when activating ``--indel``.
+You can run Mutation-Server as a standalone tool starting with CRAM/BAM files and detecting heteroplasmic and homoplasmic sites. By default BAQ is set (``--noBaq`` otherwise) and no indels  (``--indel`` otherwise) are called. Please note that currently **only deletions** are included when activating ``--indel``.
 ```
-wget https://github.com/seppinho/mutation-server/releases/download/v1.1.10/mutation-server-1.1.10.jar
+wget https://github.com/seppinho/mutation-server/releases/download/v1.1.11/mutation-server-1.1.11.jar
 
-java -jar mutation-server-1.1.10.jar  analyse-local --input <file/folder> --output <folder> --reference <fasta> --level 0.01
+java -jar mutation-server-1.1.11.jar  analyse-local --input <file/folder> --output <folder> --reference <fasta> --level 0.01 --writeVcf
 ```
 
-### Default parameter
+### Default Parameters
 
-| Parameter        | Value           | 
-| ------------- |:-------------:| 
-| MappingQuality     | 20 | 
-| BaseQuality     | 20 | 
-| AlignmentQuality     | 20 | 
+| Parameter        | Value           | Command Line Option | 
+| ------------- |:-------------:| :-------------:| 
+| MappingQuality     | 20 | `--mapQ`|
+| BaseQuality     | 20 | `--baseQ`|
+| AlignmentQuality     | 30 | `--alignQ`|
+| noBAQ     | - | `--noBAQ`|
+| Write VCF     | - | `--writeVcf`|
+| Write raw     | - | `--writeRaw`|
 
 
 ## Output Formats