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=== Analysis for QC ===
=== Analysis for QC ===
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=== Secondary analyses (with BMI) ===
=== Secondary analyses (with BMI) ===
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=== 1. Typical DIAGRAM analysis using existing association pipeline<br> ===
=== A. Typical DIAGRAM analysis using existing association pipeline<br> ===
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]]
'''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")!
=== 2. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
=== B. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
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.
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.
'''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")!
=== 3. Analysis of chromosome 20 using logistic regression score test ===
=== C. Analysis of chromosome 20 using logistic regression score test ===
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 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.
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).
=== 4. Typical DIAGRAM analysis using existing association pipeline (with BMI)<br> ===
=== D. Typical DIAGRAM analysis using existing association pipeline (with BMI)<br> ===
This is the typical DIAGRAM analysis using your current association pipeline and software including BMI adjustment. [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]
This is the typical DIAGRAM analysis using your current association pipeline and software including BMI adjustment. [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]
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=== 5. Analysis of low frequency variants using Firth bias-corrected logistic regression (with BMI) ===
=== E. 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
