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| <pre>epacts2.1/epacts single -man | | <pre>epacts2.1/epacts single -man |
| </pre> | | </pre> |
− | There are three separate association analyses to be completed: | + | To simplify the reporting process, o |
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| + | There are '''4''' separate association analyses to be completed (score and Firth, with and without adjustment for BMI): |
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| {| width="1500" border="1" align="left" cellpadding="1" cellspacing="1" | | {| width="1500" border="1" align="left" cellpadding="1" cellspacing="1" |
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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 1. Typical DIAGRAM analysis using existing association pipeline] |
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− | DIAGRAMv4_QQQ_XXX_1000G_KKK_TTT_YYY_ZZZ.txt
| + | DIAGRAMv4_iSNPs_XXX_1000G_KKK_TTT_YYY_ZZZ.txt |
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− | |-
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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]
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− | Score test
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− | All SNPs with MAC >= 1
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− | EPACTS output file
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| + | DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_TTT_YYY_ZZZ.txt |
− | DIAGRAMv4_QQQ_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts
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| |- | | |- |
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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 2. Analysis of low frequency variants using Firth bias-corrected logistic regression] |
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− | SNPs with 200 >= MAC >= 1 | + | SNPs with |
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| + | 200 >= MAC >= 1 |
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− | DIAGRAMv4_QQQ_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts
| + | DIAGRAMv4_iSNPs_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts |
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| + | DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_FBC_YYY_ZZZ.epacts |
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| |} | | |} |
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| '''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.) | | '''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.) |
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− | === A. Typical DIAGRAM analysis using existing association pipeline<br> === | + | === 1. Typical DIAGRAM analysis using existing association pipeline<br> === |
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− | This is the typical DIAGRAM analysis using your current association pipeline and software. [[File: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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− | === B. Analysis of all SNPs using logistic regression score test === | + | === 2. Analysis of low frequency variants using Firth bias-corrected logistic regression === |
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− | The score test has well-controlled type I error rate and good power for meta-analysis of balanced (equal numbers of cases and controls) studies. It is also very computationally efficient. Please run the score test using the EPACTS software. | + | The Firth bias-corrected test has well-controlled type I error rate and good power for analysis of balanced and unbalanced studies. However, it is more computationally intensive. We only run Firth on the subset of variants with 1<= MAC <= 200. |
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− | The EPACTS command for the score test analysis of all variants is: | + | To run the Firth test using the EPACTS software: |
− | <pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
| + | |
| + | epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \<br>-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10<br>B. Analysis of all SNPs using logistic regression score test<br>The score test has well-controlled type I error rate and good power for meta-analysis of balanced (equal numbers of cases and controls) studies. It is also very computationally efficient. Please run the score test using the EPACTS software. |
| + | <pre> |
| + | The EPACTS command for the score test analysis of all variants is: |
| + | epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \ |
| -test b.score -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10 | | -test b.score -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10 |
− | </pre>
| + | This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. Add the relevant additional covariates with additional "-cov" options. This assumes that the VCF files are separated by chromosomes (option -sepchr). All variants with at least one minor allele count will be analyzed (option -min-mac 1). It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10). |
− | This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. Add the relevant additional covariates with additional "-cov" options. This assumes that the VCF files are separated by chromosomes (option -sepchr). All variants with at least one minor allele count will be analyzed (option -min-mac 1). It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10). | + | </pre> |
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− | === C. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
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− |
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− | The Firth bias-corrected test has well-controlled type I error rate and good power for analysis of balanced and unbalanced studies. However, it is more computationally intensive. We only run Firth on the subset of variants with 1<= MAC <= 200.
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− |
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− | To run the Firth test using the EPACTS software:
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− | <pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
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− | -test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10</pre>
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| == 5. Report EPACTS results<br> == | | == 5. Report EPACTS results<br> == |
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