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EPACTS for DIAGRAM (view source)

Revision as of 17:06, 11 October 2012

136 bytes removed ,  17:06, 11 October 2012
→‎4.  Run EPACTS association pipeline
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<pre>epacts2.1/epacts single -man
 
<pre>epacts2.1/epacts single -man
 
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</pre>  
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There are three separate association analyses to be completed:  
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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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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline A. &nbsp;Typical DIAGRAM analysis using existing association pipeline]  
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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline 1. &nbsp;Typical DIAGRAM analysis using existing association pipeline]  
    
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DIAGRAMv4_QQQ_XXX_1000G_KKK_TTT_YYY_ZZZ.txt  
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DIAGRAMv4_iSNPs_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. &nbsp;Analysis of all SNPs using logistic regression score test]
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Score test
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All SNPs with MAC &gt;= 1
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EPACTS output file
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DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_TTT_YYY_ZZZ.txt
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DIAGRAMv4_QQQ_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts
      
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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. &nbsp;Analysis of low frequency variants using Firth bias-corrected logistic regression]  
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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 2. &nbsp;Analysis of low frequency variants using Firth bias-corrected logistic regression]  
    
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SNPs with 200 &gt;= MAC &gt;= 1  
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SNPs with
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200 &gt;= MAC &gt;= 1  
    
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DIAGRAMv4_QQQ_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts  
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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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'''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our&nbsp;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&nbsp;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>  ===
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=== 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. &nbsp; [[File:1000Genomes_march2012_imputation_analysis_plan_08312012.pdf]]
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This is the typical DIAGRAM analysis using your current association pipeline and software. &nbsp; [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]  
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=== B. Analysis of all SNPs using logistic regression score test ===
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=== 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. &nbsp;It is also very computationally efficient. &nbsp;Please run the score test using the EPACTS software.  
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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. &nbsp;However, it is more computationally intensive. &nbsp;We only run Firth on&nbsp;the subset of variants with 1&lt;= MAC &lt;= 200.  
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The EPACTS command for the score test analysis of all variants is:  
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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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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.&nbsp; It is also very computationally efficient.&nbsp; Please run the score test using the EPACTS software.
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<pre>
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The EPACTS command for the score test analysis of all variants is:
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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
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</pre>
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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).
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This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. &nbsp;Add the relevant additional covariates with additional "-cov" options. &nbsp;This assumes that the VCF files are separated by chromosomes (option -sepchr). &nbsp;All variants with at least one minor allele count will be analyzed (option -min-mac 1). &nbsp;It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10).  
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</pre>
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=== C. Analysis of low frequency variants using Firth bias-corrected logistic regression  ===
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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. &nbsp;However, it is more computationally intensive. &nbsp;We only run Firth on&nbsp;the subset of variants with 1&lt;= MAC &lt;= 200.
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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>
   
== 5. &nbsp;Report EPACTS results<br>  ==
 
== 5. &nbsp;Report EPACTS results<br>  ==
  
Clement Ma
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