From Genome Analysis Wiki
Jump to navigationJump to search
11 bytes added
, 17:29, 11 October 2012
Line 130: |
Line 130: |
| <pre>epacts2.1/epacts single -man | | <pre>epacts2.1/epacts single -man |
| </pre> | | </pre> |
− | <br> To simplify the reporting process, '''only analyze the imputed SNPs. ''' | + | <br> To simplify the reporting process, '''only analyze the imputed SNPs. ''' |
| | | |
| === Primary analyses === | | === Primary analyses === |
Line 155: |
Line 155: |
| |- | | |- |
| | | | | |
− | [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline 1. Typical DIAGRAM analysis using existing association pipeline] (with or without BMI) | + | [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline 1. Typical DIAGRAM analysis using existing association pipeline] (with or without BMI) |
| | | |
| | | | | |
Line 177: |
Line 177: |
| |- | | |- |
| | | | | |
− | [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#C._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression 2. Analysis of low frequency variants using Firth bias-corrected logistic regression] (with or without BMI) | + | [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#C._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression 2. Analysis of low frequency variants using Firth bias-corrected logistic regression] (with or without BMI) |
| | | |
| | | | | |
Line 210: |
Line 210: |
| | | |
| <br> | | <br> |
| + | |
| + | |
| | | |
| === Analyses for QC === | | === Analyses for QC === |
Line 225: |
Line 227: |
| | align="center" | '''Output Filename Format''' | | | align="center" | '''Output Filename Format''' |
| |- | | |- |
− | | [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#3._Analysis_of_chromosome_20_using_logistic_regression_score_test 3. Analysis of chromosome 20 using logistic regression score test] (without BMI) | + | | [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#3._Analysis_of_chromosome_20_using_logistic_regression_score_test 3. Analysis of chromosome 20 using logistic regression score test] (without BMI) |
| | Score test | | | Score test |
| | | | | |
Line 249: |
Line 251: |
| '''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our 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 European colleagues)<br>'''ZZZ '''indicates the name + other initials of the uploader (e.g., BFV, LJS, ABC, etc.) |
| | | |
− | | + | <br> |
| | | |
| === 1. Typical DIAGRAM analysis using existing association pipeline<br> === | | === 1. Typical DIAGRAM analysis using existing association pipeline<br> === |
Line 263: |
Line 265: |
| -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> |
− | | |
| === 3. Analysis of chromosome 20 using logistic regression score test === | | === 3. Analysis of chromosome 20 using logistic regression score test === |
| | | |