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Revision as of 21:07, 24 September 2012
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= Download EPACTS =
= Download EPACTS =
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2_01.noref_binary.2012_07_06.tar.gz here (100Mb) ].
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2_01.noref_binary.2012_07_06.tar.gz here (100Mb) ].
Requirements
Requirements
*Linux 64bit
*Linux 64bit
*Perl vX
*Perl vX
*gcc vX
*gcc vX
= Install EPACTS =
= 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
tar xzvf epacts_v2_01.noref_binary.2012_07_06.tar.gz
= Example =
= 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:
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 &
--out {OUTPUT_DIR}/test --run 2 &
</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. 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.
== Expected output ==
<br>
