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.


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


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.


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 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


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 BIOPET pipelines.

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


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.


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