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== 1. Download and install EPACTS ==
== 1. Download and install EPACTS ==
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here].
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here].
Once installed, test out the software by running a quick example using the test data provided in the ${EPACTS_DIRECTORY}/example/ directory
Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:
<pre>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
${EPACTS_DIRECTORY}/example/1000G_dummy_pheno.ped
</pre>
Run the single variant score test on the example data using this command:
<pre>${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 /net/nfsb/snowwhite/home/maclemen/test.epacts --run 2 &
</pre>
== 2. Convert the minimac or Impute2 output into VCF format ==
== 2. Convert the minimac or Impute2 output into VCF format ==
