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Jump to navigationJump to search→4. Run EPACTS association pipeline
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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline A. Typical DIAGRAM analysis using existing association pipeline]
[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline A. Typical DIAGRAM analysis using existing association pipeline]
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DIAGRAMv4_QQQ_XXX_1000G_KKK_TTT_YYY_ZZZ.txt
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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#B._Analysis_of_all_SNPs_using_logistic_regression_score_test B. Analysis of all SNPs using logistic regression score test]
[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#B._Analysis_of_all_SNPs_using_logistic_regression_score_test B. Analysis of all SNPs using logistic regression score test]
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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#C._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression C. Analysis of low frequency variants using Firth bias-corrected logistic regression]
[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#C._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression C. Analysis of low frequency variants using Firth bias-corrected logistic regression]
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DIAGRAMv4_QQQ_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts
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==== Filename key: ====
'''QQQ''': either “SNPs”, “gSNPs” or “iSNPs”. Use “SNPs” for the file, which contains both imputed and genotyped SNPs, “gSNPs” for the file which contains only genotype data, “iSNPs” for the file which contains imputed data.<br>'''XXX '''indicates a uniquely identifiable STUDY NAME: (e.g.WTCCC, DGI, DGDG, FUSION, ERGO, DUNDEE, NHS,FHS, TYROL, EUROSPAN etc.)<br>'''“_adjBMI”''' – should be present for the model with BMI adjustment<br>'''KKK '''indicates date of the 1000Genomes map, Month and year (defined as MMMYY) of the 1000Genomes map that was used e.g. MAR12<br>'''TTT '''indicates the test used to evaluate significance
*SCR = Score
*WLD = Wald
*LHR = Likelihood ratio
*FBC = Firth Bias Corrected Logistic Regression
'''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our European colleagues)<br>'''ZZZ '''indicates the name + other initials of the uploader (e.g., BFV, LJS, ABC, etc.)
=== A. Typical DIAGRAM analysis using existing association pipeline<br> ===
=== A. Typical DIAGRAM analysis using existing association pipeline<br> ===
