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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]].
=== Input Files ===
Rare Metal needs the following as input:
==== List of Studies ====
* A file with the path and name of files containing summary statistics generated by raremetalworker should be specified.
* If no such file is provided, '''Rare Metal''' will stop and report FATAL ERROR.
* Please go to [[http://genome.sph.umich.edu/wiki/Rare-Metal#List_of_Studies_2 example input for study names]] for detailed explanation and examples.
==== Groups of Variants ====
To perform gene-based or group-based burden test, groups of variants need to be provided. There are two options to provide such information:
=====From Group File =====
* A group file contains the list of groups or genes with the variants to be included in your burden tests.
* Please refer to the instruction of --groupFile option for formats and examples.
=====From Annotated VCF File =====
* '''rareMETAL''' allows user to use annotated VCF file as input for grouping of variants, which is optional to input a group file as described above.
* '''rareMETAL''' also has the option of generating a VCF file according to the pooled information from individuals studies. Then user can use their favorite annotation tools to annotate the VCF file into the INFO field. Currently, '''rareMETAL''' only support limited formats of annotated VCF file.
* A more flexible way, which is also a recommended way, is to generate a group file from the customized annotated VCF file and use that as input to '''rareMETAL'''.
* For formats of annotated VCF that '''rareMETAL''' currently support, please refer to the following [http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File annotated VCF]:
'''NOTE:''' if no grouping method is provided, then only single variant meta analysis will be performed.
=== Output Files ===
=== Output Files ===
