Changes

The basic EPACTS command for single variant tests is:  

The basic EPACTS command for single variant tests is:  

<pre>perl epacts.pl 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

<pre>epacts2/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

</pre>  

</pre>  

This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. &nbsp;The VCF files are separated by chromosomes (option -sepchr). &nbsp;All variants with at least one minor allele count will be analyzed (option -min-mac 1). &nbsp;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. &nbsp;The VCF files are separated by chromosomes (option -sepchr). &nbsp;All variants with at least one minor allele count will be analyzed (option -min-mac 1). &nbsp;It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10).  

To run the Firth test as well, use:  

To run the Firth test as well, use:  

<pre>perl epacts.pl single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] -test b.firth -pheno DISEASE -cov AGE -sepchr -anno -run 10

<pre>epacts2/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] -test b.firth -pheno DISEASE -cov AGE -sepchr -anno -run 10

</pre>  

</pre>  

For detailed description of options, use:  

For detailed description of options, use:  

<pre>perl epacts.pl single -man

<pre>epacts2/epacts.pl single -help

</pre>  

</pre>

 

== 5. &nbsp;Report association results in appropriate format<br>  ==

== 5. &nbsp;Report association results in appropriate format<br>  ==