Commit b701cbe6 authored by Moustakas's avatar Moustakas
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Create a documentation for AnnotateVcfWithBed

parent acd85018
# 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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