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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#5._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression_.28with_BMI.29 5.  Analysis of low frequency variants using Firth bias-corrected logistic regression (with BMI)]

[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#5._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression_.28with_BMI.29 5.  Analysis of low frequency variants using Firth bias-corrected logistic regression (with BMI)]  

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*Score test: &nbsp;32 seconds

*Score test: &nbsp;32 seconds

<br> Hence, we only ask for Firth test results for SNPs with MAC &lt;= 200.

<br> Hence, we only ask for Firth test results for SNPs with MAC &lt;= 200.  

 

 

 

=== 1. Typical DIAGRAM analysis using existing association pipeline<br>  ===

=== 1. Typical DIAGRAM analysis using existing association pipeline<br>  ===

This is the typical DIAGRAM analysis using your current association pipeline and software including BMI adjustment. &nbsp; [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]  

This is the typical DIAGRAM analysis using your current association pipeline and software including BMI adjustment. &nbsp; [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]  

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

'''Alternative: &nbsp;Analyze VCF and PED files using the Wald test with the EPACTS software:'''

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=== 5. Analysis of low frequency variants using Firth bias-corrected logistic regression (with BMI) ===

=== 5. Analysis of low frequency variants using Firth bias-corrected logistic regression (with BMI) ===

Again use the Firth test on EPACTS for your analysis with BMI

Again use the Firth test on EPACTS for your analysis with BMI