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, 22:05, 7 August 2013
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− | ===Options for Report Generation=== | + | ===Options for Report Generation=== |
− | * --tabix allows fast analysis when number of groups/genes of interests are less than 100.
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| * --prefix allows customized prefix for output files. | | * --prefix allows customized prefix for output files. |
− | * --maf specifies the minor allele frequency cutoff when doing gene-based or group-based burden tests. The default is maf<0.05.
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| * --longOutput allows users to output not only burden test results but also the single variant results (allele frequencies, effect sizes, and p-values) for the variants being grouped together. Please refer to the output files section for detailed explanation and examples. | | * --longOutput allows users to output not only burden test results but also the single variant results (allele frequencies, effect sizes, and p-values) for the variants being grouped together. Please refer to the output files section for detailed explanation and examples. |
| * --tabulateHits works with --hitsCutoff together to generate reports for genes that have p-value less than specified cutoff from burden tests or SKAT. The default cutoff of p-value for genes to be reported is 1.0e-06, which can be specified by --hitsCutoff option. For more explanations and examples, please go to [[http://genome.sph.umich.edu/wiki/Rare-Metal#Tabulated_Top_Hits Tabulated Top Hits]]. | | * --tabulateHits works with --hitsCutoff together to generate reports for genes that have p-value less than specified cutoff from burden tests or SKAT. The default cutoff of p-value for genes to be reported is 1.0e-06, which can be specified by --hitsCutoff option. For more explanations and examples, please go to [[http://genome.sph.umich.edu/wiki/Rare-Metal#Tabulated_Top_Hits Tabulated Top Hits]]. |
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| + | ===Miscellaneous Options=== |
| + | * --tabix allows fast analysis when number of groups/genes of interests are less than 100. |
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| == Input Files == | | == Input Files == |