Changes

<pre>epacts2.1/epacts single -man

<pre>epacts2.1/epacts single -man

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</pre>  

<br> To simplify the reporting process, '''only analyze the imputed SNPs. &nbsp;'''

<br>

=== Primary analyses  ===

=== Primary analyses  ===

-test b.score -pheno DISEASE -cov AGE -chr 20 -anno -min-mac 1 -field EC -run 10

-test b.score -pheno DISEASE -cov AGE -chr 20 -anno -min-mac 1 -field EC -run 10

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</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).  

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. &nbsp;Report EPACTS results<br>  ==

== 5. &nbsp;Report EPACTS results<br>  ==