Changes

==FallInBed==

==GREGOR==

'''FallInBed''' is a tool to test for global enrichment of trait-associated variants in experimentally annotated regulatory domains. Because all reference data are hg19, make sure your index SNP list and BED files are also in hg19 version.

'''GREGOR''' ('''G'''enomic '''R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.  

=== Download FallInBed from webpage ===  

== Get GREGOR Source Codes ==

Through this link [http://www.sph.umich.edu/csg/jich/FallInBed/  FallInBed Download], you can download a copy of FallInBed.

Through this link [http://www.sph.umich.edu/csg/jich/FallInBed/  FallInBed Download], you can download a copy of FallInBed.

   git clone git://github.com/jinchen-umich/FallInBed.git

   git clone git://github.com/jinchen-umich/FallInBed.git

Either of these two commands creates a directory which called FallInBed in the current directory.

Either of these two commands creates a directory called FallInBed in the current directory.

=== Update your copy ===

=== Update your copy ===

If you have already gotten your copy, using the following commands to update:

If you have already downloaded your copy, use the following commands to update:

   1. cd pathToYourCopy/FallInBed

   1. cd pathToYourCopy/FallInBed

   2. git pull

   2. git pull

=== Download From GitHub without Git ===

=== Download From GitHub without Git ===

If there is no git in your system, you still can download from GitHub:

If there is no git in your system, you can still download from GitHub:

# Latest Code (master branch)

# Latest Code (master branch)

#: via Website

#: via Website

#:# Goto : https://github.com/jinchen-umich/FallInBed

#:# Go to : https://github.com/jinchen-umich/FallInBed

#:# Click on the <code>Download ZIP</code> button on the right side panel.

#:# Click on the <code>Download ZIP</code> button on the right side panel.

#: via Command Line

#: via Command Line

After downloading the file, uncompress (unzip/untar) it.  The directory created will be named <code>FallInBed</code>.

After downloading the file, uncompress (unzip/untar) it.  The directory created will be named <code>FallInBed</code>.

== Build FallInBed ==

== Build GREGOR ==

To build FallInBed, copy the FallInBed package to the directory you want, and then run the following command:

To build GREGOR, copy the GREGOR package to the directory you want, and then run the following command:

   tar xzvf FallInBed.tar.gz

   tar xzvf FallInBed.tar.gz

After unzip, you can find 3 directories in "FallInBed" (./example  ./lib  ./script).

After you unzip, you can find 3 directories in "FallInBed" (./example  ./lib  ./script).

== Download reference files ==

== Download reference files ==

*Note:  SNPs that cannot be converted from rsID to chr:pos format are listed in the output file rsid.index.snp.txt.  SNPs for which there are no LD proxies or no MAF data available are listed in the output file nonannoted.index.snp.txt.

*Note:  SNPs that cannot be converted from rsID to chr:pos format are listed in the output file rsid.index.snp.txt.  SNPs for which there are no LD proxies or no MAF data available are listed in the output file nonannoted.index.snp.txt.

== Testing FallInBed ==

== Testing GREGOR ==

There is an example directory in ~/FallInBed. You can find index SNP file, 3 bed files, bed file index and example config file.

There is an example directory in ~/FallInBed. You can find index SNP file, 3 bed files, bed file index and example config file.

After change your config file, you can run a test.

After change your config file, you can run a test.

== Acknowledgements  ==

== Acknowledgements  ==

FallInBed is the result of collaborative efforts by Cristen Willer, Jin Chen, Wei Zhou, Ellen Schmidt, He Zhang, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] for any questions.

GREGOR is the result of collaborative efforts by Cristen Willer, Jin Chen, Wei Zhou, Ellen Schmidt, He Zhang, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] with any questions.