Converts a SNPTEST file to VCF.


SnptestToVcf 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 SnptestToVcf here. To generate the usage run:

java -jar <SnptestToVcf_jar> --help


This tool converts a SNPTEST file to VCF using a reference fasta. It also needs the contig of the impute file.


In order to convert a SNPTEST file to a VCF file:

java -jar <SnptestToVcf_jar> \
-i snptestOutputFile \
-o output.vcf \
-R reference.fasta \
-c contigofimputfile


Usage for SnptestToVcf:

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
--inputInfo, -i yes no Input info fields
--outputVcf, -o yes no Output vcf file
--referenceFasta, -R yes no reference fasta file
--contig, -c yes no contig of impute file


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

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


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