Description

This tool merges a VCF file with another VCF file. It provides several options on how to merge INFO fields with the same name.

Installation

VcfWithVcf 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 VcfWithVcf here. To generate the usage run:

java -jar <VcfWithVcf_jar> --help

Manual

VcfWithVcf requires an input VCF, secondary input VCF, output VCF and a reference genome fasta. It has opptions to merge fileds with the field flag -f.

Example

In order to combine input.vcf with secondary.vcf run the following command:

java -jar <VcfWithVcf_jar> \
-I input.vcf \
-s secondary.vcf \
-R reference.fa \
-o \
-output.vcf

Usage

Usage for VcfWithVcf:

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
--secondaryVcf, -s	no	no	Second Input VCF file
--outputFile, -o	yes	no	Output VCF file.
--reference, -R	yes	no	The refence that was used to call the VCF
--field, -f	no	yes (unlimited)	If only is given, the field's identifier in the output VCF will be identical to . By default we will return all values found for a given field. For INFO fields with type R or A we will take the respective alleles present in the input file. If a is supplied, a method will be applied over the contents of the field. In this case, all values will be considered. The following methods are available: - max : takes maximum of found value, only works for numeric (integer/float) fields - min : takes minimum of found value, only works for numeric (integer/float) fields - unique: takes only unique values
--match	no	no	Match alternative alleles; default true

About

VcfWithVcf 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 VcfWithVcf can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

VcfWithVcf 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 VcfWithVcf. We have had good results with this IDE.

Contact

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