Changes

For users in CSG, EPACTS can be found here:  

For users in CSG, EPACTS can be found here:  

<pre>/net/fantasia/home/hmkang/sw/epacts2.1/</pre>  

<pre>/net/fantasia/home/hmkang/sw/epacts2.1/</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:  

 

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

</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.  

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

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