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=== Primary analyses ===
=== Primary analyses (without BMI) ===
There are '''2''' separate association analyses to be completed '''without adjusting for BMI'''.
There are '''2''' separate association analyses to be completed '''without adjusting for BMI'''.
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=== Analysis for QC ===
=== Analysis for QC ===
| A. DIAGRAMv4_iSNPs_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts.gz
| A. DIAGRAMv4_iSNPs_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts.gz
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=== Secondary analyses (with BMI) ===
There are '''2''' secondary analyses''' adjusting for BMI'''.
{| width="1650" border="1" align="left" cellpadding="1" cellspacing="1"
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Association Analysis
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Statistical Test
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Subset of SNPs
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Output File Type
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Output Filename Format
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4. Typical DIAGRAM analysis using existing association pipeline (with BMI)
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Wald or likelihood ratio
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All SNPs with
MAC >= 1
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Custom file
based on DIAGRAM format
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DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_TTT_YYY_ZZZ.txt
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5. Analysis of low frequency variants using Firth bias-corrected logistic regression (with BMI)
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Firth bias-corrected
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SNPs with
200 >= MAC >= 1
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EPACTS output file
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DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_FBC_YYY_ZZZ.epacts.gz
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'''Please send the 2 Primary analyses and the QC analysis when complete.'''
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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]]
==== 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: ====
This will be a good way to check if your VCF and PED files are correctly formatted for EPACTS.
As preparation for the Firth test analysis, we encourage you to analyze the data using the Wald test first, since it is computationally faster. This will be a good way to check if your VCF and PED files are correctly formatted for EPACTS and resolve any problems you may have with your imputation or input files.
<pre>epacts.v2.2.0.20121026 /epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>epacts.v2.2.0.20121026 /epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-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")!
=== 2. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
=== 2. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -field EC -run 10
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -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")!
=== 3. Analysis of chromosome 20 using logistic regression score test ===
=== 3. Analysis of chromosome 20 using logistic regression score test ===
-test b.score -pheno DISEASE -cov AGE -chr 20 -anno -min-mac 1 -field EC -run 10
-test b.score -pheno DISEASE -cov AGE -chr 20 -anno -min-mac 1 -field EC -run 10
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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> ===
This is the typical DIAGRAM analysis using your current association pipeline and software including BMI adjustment. [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]
==== Alternative: Analyze VCF and PED files using the Wald test with the EPACTS software: ====
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=== 5. 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
== 5. Report EPACTS results<br> ==
== 5. Report EPACTS results<br> ==
