Test EPACTS for DIAGRAM

Download EPACTS

EPACTS is available for download here (100Mb) .

Requirements

• Linux (e.g. Ubuntu)
• Perl vX
• gcc vX

Install EPACTS

Uncompress EPACTS package to the directory you would like to install

 tar xzvf epacts_v2_01.noref_binary.2012_07_06.tar.gz

Example

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.