Test EPACTS for DIAGRAM
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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.