From b701cbe6dc402ee3e1c9e7416463ccdff3403c4f Mon Sep 17 00:00:00 2001
From: Ioannis Moustakas <i.moustakas@lumc.nl>
Date: Tue, 5 Jul 2016 15:46:01 +0200
Subject: [PATCH] Create a documentation for AnnotateVcfWithBed

---
 docs/tools/AnnotateVcfWithBed.md | 39 ++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/docs/tools/AnnotateVcfWithBed.md b/docs/tools/AnnotateVcfWithBed.md
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+# AnnotateVcfWithBed 
+
+## Introduction
+ This tool to annotates a vcf file with input from a bed file
+
+## Example
+To get the help menu:
+~~~
+Usage: AnnotateVcfWithBed [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <vcf file> | --inputFile <vcf file>
+        Input is a required file property
+  -B <bed file> | --bedFile <bed file>
+        Bedfile is a required file property
+  -o <vcf file> | --output <vcf file>
+        out is a required file property
+  -f <name of field in vcf file> | --fieldName <name of field in vcf file>
+        Name of info field in new vcf file
+  -d <name of field in vcf file> | --fieldDescription <name of field in vcf file>
+        Description of field in new vcf file
+  -t <name of field in vcf file> | --fieldType <name of field in vcf file>
+        Description of field in new vcf file
+~~~
+
+To run the tool:
+~~~
+biopet tool AnnotateVcfWithBed -I myVcf.vcf -B myBed.bed -o myannotatedVcf.vcf  
+~~~
+
+
+## Results
+The result of this tool will be a vcf file with an extra field with annotation
+
-- 
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