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 a pipeline, for example the SASC team's biowdl 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: sasc@lumc.nl.