This tool allows for the generation of a consensus sequences of polyploid genomes from NGS reads.
Make sure you meet the requirements. You need to have the Java runtime environment installed (version 1.8 and above) and you need to have the JAVA_HOME variable in your system settings. You can download the java enviroment at Java.
You can now run the program by executing:
$ java -jar polytools-<version>.jar <command> <option1> <option2> ..
To see which commands you can run.
Try:
$ java -jar polytools-<version>.jar --help
Or run:
$ java -jar polytools-<version>.jar -examples
Now you see some example commands that explain the functionality of the program.
You can find more examples and explanation of the commands in the manual at the Project Wiki under documents.
- Java runtime environment (verion 1.8 and above) Java.
This consensus sequence generator includes:
- Heterozygous support
- Polyploid support
- Labeling
- Regions
- Filters
- Zip VCF support
Verified VCF versions and verified variant callers (e.g. source)
- VCF v4.1
- gatk
- Pilon v1.22
- Freebays v1.2.0
- VCF v4.2
- Freebays v1.2.0
Download the master. Open the project in your favorite IDE. Make sure you have gradle available in your IDE, see Built with.
Running the tests is done by Gradle.
Try:
> ./gradlew test
- BcfTools - Utilities for variant calling and manipulating VCFs and BCF
- JVARKIT - Java utilities for Bioinformatics
- VCF-kit - Command-line based utilities for performing analysis on VCF files.
A overview of the releases can be found
Arjan Seijs Bas Jenneboer Erik Sennema Koen du Buf Regi Veerhuis