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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] \
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10
</pre>
3. Analysis of all SNPs using logistic regression score test<br>The score test has well-controlled type I error rate and good power for meta-analysis of balanced (equal numbers of cases and controls) studies. It is also very computationally efficient. Please run the score test using the EPACTS software.
The EPACTS command for the score test analysis of all variants is:
The EPACTS command for the score test analysis of all variants is:
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.score -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10
-test b.score -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10
</pre>
</pre>
This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. Add the relevant additional covariates with additional "-cov" options. This assumes that the VCF files are separated by chromosomes (option -sepchr). All variants with at least one minor allele count will be analyzed (option -min-mac 1). It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10).
== 5. Report EPACTS results<br> ==
== 5. Report EPACTS results<br> ==
