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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].
For users in CSG, EPACTS can be found here:
For users in CSG, EPACTS can be found here:
<pre>/net/fantasia/home/hmkang/sw/epacts2/</pre>
<pre>/net/fantasia/home/hmkang/sw/epacts2/</pre>
<br> 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>$ epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
$ epacts2/example/1000G_dummy_pheno.ped
</pre>
</pre>
<br> Run the single variant score test on the example data using this command:
<br> Run the single variant score test on the example data using this command:
<pre>${EPACTS_DIR}/epacts single
<pre>$ epacts2/epacts single
--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
--vcf epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped
--ped epacts2/example/1000G_dummy_pheno.ped
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno
--out {OUTPUT_DIR}/test --run 2 &
--out {OUTPUT_DIR}/test --run 2 &
