Statistical associations using the ADAM genomics analysis platform. The currently supported operations are Genome Wide Association using Linear and Logistic models with either Dominant or Additive assumptions.
To build, install Maven. Then (once in the gnocchi directory) run:
mvn package
Maven will automatically pull down and install all of the necessary dependencies.
Occasionally, building in Maven will fail due to memory issues. You can work around this
by setting the MAVEN_OPTS environment variable to -Xmx2g -XX:MaxPermSize=1g.
Gnocchi is built on top of Apache Spark. If you are just evaluating locally, you can use a prebuilt Spark distribution. If you'd like to use a cluster, refer to Spark's cluster overview.
Once Spark is installed, set the environment variable SPARK_HOME to point to the Spark
installation root directory.
The target binaries are complied to the bin/ directory. Add them to your path with
echo "export PATH=[GNOCCHI INSTALLATION DIR]/gnocchi/bin:\$PATH" >> $HOME/.bashrc
source $HOME/.bashrc
You can then run gnocchi via gnocchi-submit, or open a shell using gnocchi-shell.
Test data is included. You can run with the test data by running:
gnocchi-submit regressPhenotypes testData/5snps10samples.vcf testData/10samples5Phenotypes2covars.txt ADDITIVE_LINEAR testData/associations -saveAsText -phenoName pheno1 -covar -covarFile testData/10samples5Phenotypes2covars.txt -covarNames pheno4,pheno5
Format phenotypes in a CSV. Both comma and tabs are accepted as delimiters.
SampleID pheno1 pheno2
00001 0.001 0.002
Note: phenotypes and covariates must be numerical. For nominal scale data (i.e. categorical data), binarize. For ordinal scale data, convert to integers.
This project is released under an Apache 2.0 license.