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This is the typical DIAGRAM analysis using your current association pipeline and software. [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]
This is the typical DIAGRAM analysis using your current association pipeline and software. [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]
For frequently asked questions regarding the file format, please see: [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#Results_FIle_Clarifications genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#Results_FIle_Clarifications]
==== 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: ====
-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
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'''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 ===
