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<pre>epacts2.1/epacts single -man
<pre>epacts2.1/epacts single -man
</pre>
</pre>
To simplify the reporting process, o
<br> To simplify the reporting process, '''only analyze the imputed SNPs. '''
There are '''4''' separate association analyses to be completed (sco
=== Primary analyses ===
There are '''4''' separate association analyses to be completed.
{| width="1650" border="1" align="left" cellpadding="1" cellspacing="1"
{| width="1650" border="1" align="left" cellpadding="1" cellspacing="1"
|
|
All SNPs with MAC >= 1
All SNPs with
MAC >= 1
|
|
Custom file
Custom file
based on DIAGRAM format
based on DIAGRAM format
<br>
<br>
=== Analyses for QC ===
For quality control, please run an additional analysis using EPACTS on all SNPs for chromosome 20 only using the '''SCORE''' test without BMI adjustment. These results will be used to compare with results from the primary analyses, to ensure the new EPACTS software has been run correctly.
{| width="1650" border="1" cellpadding="1" cellspacing="1" align="center"
|-
| align="center" | '''Association Analysis'''
| align="center" | '''Statistical Test'''
| align="center" | '''Subset of SNPs'''
| align="center" | '''Output File Type'''
| align="center" | '''Output Filename Format'''
|-
| 3. Analysis of chromosome 20 using logistic regression score test
| Score test
|
Chromosome 20 SNPs
with MAC >= 1
| EPACTS output file
| A. DIAGRAMv4_iSNPs_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts
|}
<br>
<br>
==== Filename key: ====
==== Filename key: ====
'''QQQ''': either “SNPs”, “gSNPs” or “iSNPs”. Use “SNPs” for the file, which contains both imputed and genotyped SNPs, “gSNPs” for the file which contains only genotype data, “iSNPs” for the file which contains imputed data.<br>'''XXX '''indicates a uniquely identifiable STUDY NAME: (e.g.WTCCC, DGI, DGDG, FUSION, ERGO, DUNDEE, NHS,FHS, TYROL, EUROSPAN etc.)<br>'''“_adjBMI”''' – should be present for the model with BMI adjustment<br>'''KKK '''indicates date of the 1000Genomes map, Month and year (defined as MMMYY) of the 1000Genomes map that was used e.g. MAR12<br>'''TTT '''indicates the test used to evaluate significance
'''iSNPs''' indicates the file contains imputed SNPs only<br>'''XXX '''indicates a uniquely identifiable STUDY NAME: (e.g.WTCCC, DGI, DGDG, FUSION, ERGO, DUNDEE, NHS,FHS, TYROL, EUROSPAN etc.)<br>'''“_adjBMI”''' – should be present for the model with BMI adjustment<br>'''KKK '''indicates date of the 1000Genomes map, Month and year (defined as MMMYY) of the 1000Genomes map that was used e.g. MAR12<br>'''TTT '''indicates the test used to evaluate significance
*SCR = Score
*SCR = Score
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</pre>
The EPACTS command for the score test analysis of all variants is:
=== 3. 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 EPACTS command for the score test analysis of chromosome 20 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 -chr 20 -anno -min-mac 1 -run 10
