Changes

</pre>

</pre>

= Getting started in EPACTS with an example =

= Getting started in EPACTS with an 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>$ epacts2/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz

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

$ epacts2/example/1000G_dummy_pheno.ped

$ epacts2.1/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/epacts single \

<pre>$ epacts2.1/epacts single \

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

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

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

--ped epacts2.1/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 &amp;

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