Create a documentation for AnnotateVcfWithBed

docs/tools/AnnotateVcfWithBed.md

+# 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
+