Changes

==== Alternative:  Analyze VCF and PED files using the Wald test with the EPACTS software:  ====

==== Alternative:  Analyze VCF and PED files using the Wald test with the EPACTS software:  ====

As preparation for the Firth test analysis, we encourage you to analyze the data using the Wald test first, since it is computationally faster.  This will be a good way to check if your VCF and PED files are correctly formatted for EPACTS and resolve any problems you may have with your imputation or input files.  

As preparation for the Firth test analysis, we encourage you to analyze the data using the Wald test first, since it is computationally much faster.  This will be a good way to check if your VCF and PED files for every chromosome are correctly formatted for EPACTS and resolve any problems you may have with your imputation or input files.  

<pre>epacts.v2.2.0.20121026 /epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \

<pre>epacts.v2.2.0.20121026 /epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \

-test b.wald -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -field EC -run 10

-test b.wald -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -field EC -run 10

</pre>  

</pre>  

'''Important:''' To analyze dosages (not genotypes), you must specify the dosage field with the "--field EC" option. Without this option, you will be analyzing the hard genotypes (i.e. --field option defaults to "GT" or "genotypes")!  

'''Important:''' To analyze dosages (not genotypes), you must specify the dosage field with the "--field EC" option. Without this option, you will be analyzing the hard genotypes (i.e. --field option defaults to "GT" or "genotypes")!

=== B. Analysis of low frequency variants using Firth bias-corrected logistic regression  ===

=== B. Analysis of low frequency variants using Firth bias-corrected logistic regression  ===