Description

This tool corrects the reference alleles in a VCF file. Some tools switch the REF and ALT alleles when creating a vcf. This tool checks what the reference allele is at the given position. It then checks whether this matches up with the REF and ALT column and switches them if necessary.

Installation

CorrectRefAlleles 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 CorrectRefAlleles here. To generate the usage run:

java -jar <CorrectRefAlleles_jar> --help

Manual

This tool needs a reference genome to check if the stated REF allele at a given position is correct. The contig names of the reference and the input VCF should match.

Example

To check if input.vcf REF and POS columns matches with reference.fa and give the corrected vcf as output.vcf:

java -jar <CorrectRefAlleles_jar> \
-I input.vcf \
-o output.vcf \
-R reference.fa

Usage

Usage for CorrectRefAlleles:

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
--input, -I	yes	no	input vcf file
--output, -o	yes	no	output vcf file
--referenceFasta, -R	yes	no	Reference fasta file

About

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

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

Contact

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