Changes

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>$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz

<pre>$ epacts.v2.2.0.20121026/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz

$ epacts2.1/example/1000G_dummy_pheno.ped

$ epacts.v2.2.0.20121026/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>$ epacts2.1/epacts single  

<pre>$ epacts.v2.2.0.20121026/epacts single  

--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz  

--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz  

--ped epacts2.1/example/1000G_dummy_pheno.ped  

--ped epacts2.1/example/1000G_dummy_pheno.ped  

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.  

A more detailed description of the example can be found [http://genome.sph.umich.edu/wiki/Test_EPACTS_for_DIAGRAM here].  

A more detailed description of the example can be found [http://genome.sph.umich.edu/wiki/Test_EPACTS_for_DIAGRAM here].

== 2. &nbsp;Prepare VCF file with genotypes / dosages  ==

== 2. &nbsp;Prepare VCF file with genotypes / dosages  ==