Changes

'''Rare Metal''' is a tool for gene-based meta-analysis, based upon summary statistics generated from individual data using [http://genome.sph.umich.edu/wiki/Rare-Metal-Worker '''Rare Metal Worker''']. Another implementation of the same methods in R-package can be found [http://genome.sph.umich.edu/wiki/RareMETALS '''RareMetals'''].

'''rareMETAL''' is a tool for gene-based meta-analysis, based upon summary statistics generated from individual data using [http://genome.sph.umich.edu/wiki/Rare-Metal-Worker '''Rare Metal Worker''']. Another implementation of the same methods in R-package can be found [http://genome.sph.umich.edu/wiki/RareMETALS '''RareMetals'''].

If you have any questions, please contact: sfengsph at umich dot edu

If you have any questions, please contact: sfengsph at umich dot edu

== Key Features ==

== Key Features ==

'''Rare Metal''' has the following features:

'''rareMETAL''' has the following features:

* '''Rare Metal''' performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold.  

* '''rareMETAL''' performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold.  

* '''Rare Metal''' performs single variant metal-analysis by default.  

* '''rareMETAL''' performs single variant metal-analysis by default.  

* '''Rare Metal''' allows customized groups of variants to be tested.

* '''rareMETAL''' allows customized groups of variants to be tested.

* '''Rare Metal''' allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.

* '''rareMETAL''' allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.

* '''Rare Metal''' generated QQ plots and manhattan plots by default.

* '''rareMETAL''' generated QQ plots and manhattan plots by default.

== Software Download and Installation ==

== Software Download and Installation ==

=====From Annotated VCF File =====

=====From Annotated VCF File =====

* '''Rare Metal''' 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''' allows user to use annotated VCF file as input for grouping of variants, which is optional to input a group file as described above.

* '''Rare Metal''' 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, '''Rare Metal''' only support limited formats of annotated VCF file.  

* '''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 '''Rare Metal'''.

* 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 '''Rare Metal''' currently support, please refer to the following [http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File  annotated VCF]:

* 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.

'''NOTE:''' if no grouping method is provided, then only single variant meta analysis will be performed.