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EPACTS for DIAGRAM (view source)

Revision as of 10:34, 19 September 2012

1,086 bytes added ,  10:34, 19 September 2012
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#Convert the minimac or Impute2 output into VCF format  
 
#Convert the minimac or Impute2 output into VCF format  
 
#Prepre PED file for phenotypes and covariates  
 
#Prepre PED file for phenotypes and covariates  
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#Run EPACTS association pipeline
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#Run EPACTS association pipeline  
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#Report association results in appropriate format
    
== 1.  Download and install EPACTS  ==
 
== 1.  Download and install EPACTS  ==
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13291 NA06997 NA06986 NA07045 2 2 107.53 53.1
 
13291 NA06997 NA06986 NA07045 2 2 107.53 53.1
 
</pre>  
 
</pre>  
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Alternatively, you can prepare a PED file without a header, and include a corresponding DAT file describing the column headers.
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Alternatively, you can prepare a PED file without a header, and include a corresponding DAT file describing the column headers.  
 
<pre>13281 NA12344 NA12347 NA12348 1 1 94.17 66.1
 
<pre>13281 NA12344 NA12347 NA12348 1 1 94.17 66.1
 
13281 NA12347 0 0 1 1 109.54 44.0
 
13281 NA12347 0 0 1 1 109.54 44.0
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M QT
 
M QT
 
M AGE
 
M AGE
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</pre>
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</pre>  
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== 4. &nbsp;Run EPACTS association pipeline  ==
 
== 4. &nbsp;Run EPACTS association pipeline  ==
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<pre>perl epacts.pl single -man
 
<pre>perl epacts.pl single -man
 
</pre>  
 
</pre>  
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<br>
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== 5. &nbsp;Report association results in appropriate format<br> ==
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Once the EPACTS pipeline has completed, you will find all of the results in the ''.epacts ''file. &nbsp;Here is an example:
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<pre>#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
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20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA
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20 68319 68319 20:68319_C/A_Upstream:DEFB125 266 0 1 0 NA NA
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20 68396 68396 20:68396_C/T_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA
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20 76635 76635 20:76635_A/T_Intron:DEFB125 266 0 1 0 NA NA
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20 76689 76689 20:76689_T/C_Synonymous:DEFB125 266 0 1 0 NA NA
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20 76690 76690 20:76690_T/C_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA
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20 76700 76700 20:76700_G/A_Nonsynonymous:DEFB125 266 0 1 0 NA NA
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20 76726 76726 20:76726_C/G_Nonsynonymous:DEFB125 266 0 1 0 NA NA
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20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587
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</pre>
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You will need to parse the information into the format as required here [NEED FINAL DRAFT OF ASSOCIATION ANALYSIS FILE AND&nbsp;COLUMN&nbsp;SPECIFICATIONS].
Clement Ma
216

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