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== 4. Run EPACTS association pipeline ==
== 4. Run EPACTS association pipeline ==
There are three separate association analyses to be completed:
There are three separate association analyses to be completed:
{| width="1500" border="1" align="left" cellpadding="1" cellspacing="1"
{| width="1500" border="1" align="left" cellpadding="1" cellspacing="1"
|-
|-
! scope="col" | Association Analysis
! scope="col" | Association Analysis
! scope="col" | Statistical Test
! scope="col" | Statistical Test
! scope="col" | Subset of SNPs
! scope="col" | Subset of SNPs
! scope="col" | Output File Type
! scope="col" | Output File Type
! scope="col" | Output Filename Format
! scope="col" | Output Filename Format
|-
|-
| A. Typical DIAGRAM analysis using existing association pipeline
| A. Typical DIAGRAM analysis using existing association pipeline
| Wald or likelihood ratio
| Wald or likelihood ratio
| All SNPs with min MAC >= 1
| All SNPs with min MAC >= 1
| Custom file based on DIAGRAM format
| Custom file based on DIAGRAM format
| DIAGRAMv4_QQQ_XXX_1000G_KKK_YYY_ZZZ.txt
| DIAGRAMv4_QQQ_XXX_1000G_KKK_YYY_ZZZ.txt
|-
|-
| B. Analysis of all SNPs using logistic regression score test
| B. Analysis of all SNPs using logistic regression score test
| Score test
| Score test
| All SNPs with min MAC >= 1
| All SNPs with min MAC >= 1
| EPACTS output file
| EPACTS output file
| DIAGRAMv4_QQQ_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts
| DIAGRAMv4_QQQ_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts
|-
|-
| C. Analysis of low frequency variants using Firth bias-corrected logistic regression
| C. Analysis of low frequency variants using Firth bias-corrected logistic regression
| Firth bias-corrected
| Firth bias-corrected
| SNPs with 200 >= MAC >= 1
| SNPs with 200 >= MAC >= 1
| EPACTS output file
| EPACTS output file
| DIAGRAMv4_QQQ_XXX_1000G_KKK_FIR_YYY_ZZZ.epacts
| DIAGRAMv4_QQQ_XXX_1000G_KKK_FIR_YYY_ZZZ.epacts
|}
|}
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<br>
=== A. Typical DIAGRAM analysis using existing association pipeline<br> ===
This is the typical DIAGRAM analysis using your current association pipeline and software. Please follow the format here '''[INSERT PROTOCOL]'''.
=== A. Typical DIAGRAM analysis using existing association pipeline<br> ===
=== B. Analysis of all SNPs 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 EPACTS command for the score test analysis of all variants is:
The EPACTS command for the score test analysis of all variants is:
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>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
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).
=== C. Analysis of low frequency variants using Firth bias-corrected logistic regression ===
=== C. 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.
To run the Firth test using the EPACTS software:
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] \
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10
</pre>
</pre>
<br> For detailed description of options, use:
For detailed description of options, use:
<pre>epacts2.1/epacts single -man
<pre>epacts2.1/epacts single -man
</pre>
</pre>
