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===Options for Report Generation===
===Options for Report Generation===
* --prefix allows customized prefix for output files.
* --prefix allows customized prefix for output files.
* --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]].
===Miscellaneous Options===
* --tabix allows fast analysis when number of groups/genes of interests are less than 100.
== Input Files ==
== Input Files ==
