1,120
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Single Variant Tests
== Lastest ChangeLog ==
== Lastest ChangeLog ==
* Dec 15th, 2016 : EPACTS v3.3.0 release (github)
** Moved the repository into github
** Some major fixes in handling large sample size (>18,000)
** Other minor bug fixes
* July 10th, 2014 : EPACTS v3.2.6 release
* July 10th, 2014 : EPACTS v3.2.6 release
** Minor bug fix in epacts-make-kin
** Minor bug fix in epacts-make-kin
== Obtaining EPACTS ==
== Obtaining EPACTS ==
* The official release of EPACTS software is available at /net/csgsites/csg-old/kang/epacts/download/ .
* The official release of EPACTS software is available at https://github.com/statgen/EPACTS
** From the CSG cluster, it is available at /net/fantasia/home/bin/epacts/
** From the CSG cluster, it is available at /net/fantasia/home/bin/epacts/
* Note that R (version 2.10 or higher) and gnuplot (version 4.2 or higher) must be installed in order to run EPACTS correctly.
* Note that R (version 2.10 or higher) and gnuplot (version 4.2 or higher) must be installed in order to run EPACTS correctly.
| Firth Bias-Corrected Logistic Likelihood Ratio Test
| Firth Bias-Corrected Logistic Likelihood Ratio Test
| Clement Ma
| Clement Ma
|-
| b.spa2
| Binary
| YES <br>
| Moderate
| Saddlepoint Approximation Method
| Shawn Lee & Rounak Dey
|-
|-
| b.lrt
| b.lrt
| Linear Wald Test
| Linear Wald Test
| Hyun Min Kang <br> (as implemented in lm in R)
| Hyun Min Kang <br> (as implemented in lm in R)
|-
|-
| q.linear
| q.linear
If you want to use EPACTS in an Ubuntu platform, following the step below
If you want to use EPACTS in an Ubuntu platform, following the step below
$ git clone https://github.com/statgen/EPACTS.git
$ cd EPACTS
$ ./configure --prefix [/path/to/install]
$ make
$ make install
(Important Note: '''make sure to specify --prefix=/path/to/install''' to avoid installing to the default path /usr/local/, which you may not have the permission. /home/your_userid/epacts might be a good one, if you are not sure where to install)
(Important Note: '''make sure to specify --prefix=/path/to/install''' to avoid installing to the default path /usr/local/, which you may not have the permission. /home/your_userid/epacts might be a good one, if you are not sure where to install)
In order to use EPACTS in the CSG cluster, you do not need to install them. You can directly use or make a copy of the in-house release version at
In order to use EPACTS in the CSG cluster, you do not need to install them. You can directly use or make a copy of the in-house release version at
/net/fantasia/home/hmkang/bin/epacts/
/net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts/
* If you want to access previous versions, visit http://csg-old.sph.umich.edu/kang/epacts/download
== Getting Started With Examples ==
== Getting Started With Examples ==
If you are using EPACTS from the CSG cluster, please set the following environment variable
If you are using EPACTS from the CSG cluster, please set the following environment variable
EPACTS_DIR=/net/fantasia/home/hmkang/bin/epacts (in bash)
EPACTS_DIR=/net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts (in bash)
setenv EPACTS_DIR /net/fantasia/home/hmkang/bin/epacts (in csh)
setenv EPACTS_DIR /net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts (in csh)
If you downloaded EPACTS binary and please set EPACTS_DIR to the full path of the downloaded and uncompressed directory.
If you downloaded EPACTS binary and please set EPACTS_DIR to the full path of the downloaded and uncompressed directory.
