genome / mendelscan

Analyze exome data for Mendelian disorders. Still in alpha-testing.

MendelScan

Overview

Please see the official site for MendelScan, on GMT, for detailed information.

Releases

Please see the releases page for official releases.

Build

You can build the Java source by running ant compile or a JAR file by running ant dist.

Run

You can run the JAR file on the commandline like any Java JAR file, e.g. java -jar ./MendelScan.jar.

Source Documentation

Javadoc is published on the GitHub page.

Example

Included in the repository is an example data set using 1000 Genomes data.

tar -zxvf example_data.tar.gz
cd example_data
java -jar MendelScan.jar score variants.vcf \
    --vep-file annotation.vep --ped-file family.ped --gene-file gene-expression.txt \
    --output-file mendelscan.tsv --output-vcf mendelscan.vcf