Test EPACTS for DIAGRAM

1.  Download and install EPACTS

EPACTS is available for download here.

If you want to use EPACTS in an Ubuntu platform, following the step below

• Download EPACTS binary at http://www.sph.umich.edu/csg/kang/epacts/download/epacts2.noref_binary.2012_07_03.tar.gz (94MB)
• Uncompress EPACTS package to the directory you would like to install

 tar xzvf epacts2.noref_binary.2012_07_03.tar.gz

• Download the reference FASTA files by running the following commands

 cd epacts2/
 ./ref_download.sh (Or copy the FASTA and index file locally you have to ${EPACTS_DIR}/ext/ref/)

• Perform a test run by running the following command

 example/test_run_epacts.sh

Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:

${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz

${EPACTS_DIRECTORY}/example/1000G_dummy_pheno.ped

Run the single variant score test on the example data using this command:

${EPACTS_DIR}/epacts single 
--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 
--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped 
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno 
--out {OUTPUT_DIR}/test --run 2 &

This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001.  The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX.  The output file directory prefix is {OUTPUT_DIR}/test.  Finally, EPACTS will run the analysis in parallel on 2 CPUs.