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, 12:00, 14 December 2012
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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]] |
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| + | 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] |
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| ==== 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: ==== |
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| -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")! |
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| === B. Analysis of low frequency variants using Firth bias-corrected logistic regression === | | === B. Analysis of low frequency variants using Firth bias-corrected logistic regression === |