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, 17:54, 1 October 2012
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| -test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10</pre> | | -test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10</pre> |
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− | == 5. Report association results in appropriate format<br> == | + | == 5. Report EPACTS results<br> == |
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− | Once the EPACTS pipeline has completed, you will find all of the results in the ''.epacts.gz'' file. Here is an example of score test results:
| + | For analysis B and C, please upload the two .epacts.gz files to the FTP server: |
− | <pre>#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE | + | |
− | 20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA | + | #'''Score test:''' DIAGRAMv4_QQQ_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts.gz |
− | 20 68319 68319 20:68319_C/A_Upstream:DEFB125 266 0 1 0 NA NA | + | #'''Firth test: ''' DIAGRAMv4_QQQ_XXX_1000G_KKK_FIR_YYY_ZZZ.epacts.gz |
− | 20 68396 68396 20:68396_C/T_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA | + | |
− | 20 76635 76635 20:76635_A/T_Intron:DEFB125 266 0 1 0 NA NA | + | Here's an example score test .epacts file |
− | 20 76689 76689 20:76689_T/C_Synonymous:DEFB125 266 0 1 0 NA NA | + | <pre>$ head test.epacts |
− | 20 76690 76690 20:76690_T/C_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA | + | #CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE N.CASE N.CTRL AF.CASE AF.CTRL |
− | 20 76700 76700 20:76700_G/A_Nonsynonymous:DEFB125 266 0 1 0 NA NA | + | 20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA |
− | 20 76726 76726 20:76726_C/G_Nonsynonymous:DEFB125 266 0 1 0 NA NA | + | 20 68319 68319 20:68319_C/A_Upstream:DEFB125 266 0 1 0 NA NA NA NA NA NA |
− | 20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587 | + | 20 68396 68396 20:68396_C/T_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA |
− | </pre> | + | 20 76635 76635 20:76635_A/T_Intron:DEFB125 266 0 1 0 NA NA NA NA NA NA |
− | You will need to parse the information into the format as required here ['''NEED FINAL DRAFT OF ASSOCIATION ANALYSIS FILE AND COLUMN SPECIFICATIONS'''].
| + | 20 76689 76689 20:76689_T/C_Synonymous:DEFB125 266 0 1 0 NA NA NA NA NA NA |
| + | 20 76690 76690 20:76690_T/C_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA |
| + | 20 76700 76700 20:76700_G/A_Nonsynonymous:DEFB125 266 0 1 0 NA NA NA NA NA NA |
| + | 20 76726 76726 20:76726_C/G_Nonsynonymous:DEFB125 266 0 1 0 NA NA NA NA NA NA |
| + | 20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587 145 121 0.013793 0.0082645 |
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| + | </pre> |