Description

This tool to annotates a vcf file using the input from a bed file. The name, description and type of vcf field can be set with the tool.

Installation

AnnotateVcfWithBed requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.

Download the latest version of AnnotateVcfWithBed here. To generate the usage run:

java -jar <AnnotateVcfWithBed_jar> --help

Manual

The result of this tool will be a vcf file with an extra field with annotation. The name, description and type of vcf field can be set with the tool.

Example

To annotate input.vcf with inputBed.bed and name the field BedAnnotation

java -jar <AnnotateVcfWithBed_jar> \
-I input.vcf \
-B inputBed.bed \
-o output.vcf \
-f BedAnnotation

Usage

Usage for AnnotateVcfWithBed:

Option Required Can occur multiple times Description
--log_level, -l no no Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
--help, -h no no Print usage
--version, -v no no Print version
--inputFile, -I yes no Input VCF file. Mandatory field
--bedFile, -B yes no Input Bed file. Mandatory field
--output, -o yes no Output VCF file. Mandatory field
--fieldName, -f yes no Name of info field in new vcf file
--fieldDescription, -d no no Description of field in new vcf file
--fieldType, -t no no Type of field in new vcf file. Can be 'Integer', 'Flag', 'Character', 'Float'

About

AnnotateVcfWithBed is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contributing

The source code of AnnotateVcfWithBed can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

AnnotateVcfWithBed is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on AnnotateVcfWithBed. We have had good results with this IDE.

Contact

For any question related to AnnotateVcfWithBed, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.