Changes

== 1.  Download and install EPACTS ==

# Download 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].

 

* 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   

 

*Linux (e.g. Ubuntu)

*Perl vX

 

 

 

Uncompress EPACTS package to the directory you would like to install   

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

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

 

# 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:  

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

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

--out {OUTPUT_DIR}/test --run 2 &amp;

--out {OUTPUT_DIR}/test --run 2 &amp;

</pre>  

</pre>  

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

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