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| * --maf specifies the minor allele frequency cutoff when doing gene-based or group-based burden tests. The default is maf<0.05. | | * --maf specifies the minor allele frequency cutoff when doing gene-based or group-based burden tests. The default is maf<0.05. |
| * --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 [[https://statgen.sph.umich.edu/wiki/Raremetal#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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| === Output Files === | | === Output Files === |