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== 4. Run EPACTS association pipeline ==
== 4. Run EPACTS association pipeline ==
For detailed description of options, use:
<pre>epacts2.1/epacts single -man
</pre>
There are three separate association analyses to be completed:
There are three separate association analyses to be completed:
To run the Firth test using the EPACTS software:
To run the Firth test using the EPACTS software:
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10</pre>
</pre>
== 5. Report association results in appropriate format<br> ==
== 5. Report association results in appropriate format<br> ==
