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== 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
** Minor bug fix in epacts-make-kin
* March 11th, 2014 : EPACTS v3.2.5 release
** EMMAX-SKAT is implemented with major bug fix
* November 21th, 2013 : EPACTS v3.2.4 release
* November 21th, 2013 : EPACTS v3.2.4 release
** Fixed a number of minor bugs (more comprehensive fix is still pending)
** Fixed a number of minor bugs (more comprehensive fix is still pending)
== Obtaining EPACTS ==
== Obtaining EPACTS ==
* The official release of EPACTS software is available at http://www.sph.umich.edu/csg/kang/epacts/ .
* 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.
bgzip input.vcf ## this command will produce input.vcf.gz
bgzip input.vcf ## this command will produce input.vcf.gz
tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi
tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi
* If the VCF file is separated by chromosome, the VCF file must contain the string "chr1" in the chromosome 1 file, and corresponding chromosome name for other chromosomes.
* If the VCF file is separated by chromosome, the VCF file specified in the input argument must contain the string "chr1" in the chromosome 1 file, and corresponding chromosome name for other chromosomes. Thus, the files names should be like <code>[prefix]chr1[suffix].vcf.gz</code>, <code>[prefix]chr2[suffix].vcf.gz</code>, ..., <code>[prefix]chr22[suffix].vcf.gz</code>, <code>[prefix]chrX[suffix].vcf.gz</code>.
* Sample IDs in the VCF file must be consistent to those from PED file
* Sample IDs in the VCF file must be consistent to those from PED file
* Currently EPACTS only support bi-allelic variants, but it handles SNPs, INDELs, snd SVs.
* Currently EPACTS only support bi-allelic variants, but it handles SNPs, INDELs, snd SVs.
== Full ChangeLog ==
== Full ChangeLog ==
* July 10th, 2014 : EPACTS v3.2.6 release
** Minor bug fix in epacts-make-kin
* March 11th, 2014 : EPACTS v3.2.5 release
** EMMAX-SKAT is implemented with major bug fix
* November 21th, 2013 : EPACTS v3.2.4 release
* November 21th, 2013 : EPACTS v3.2.4 release
** Fixed a number of minor bugs (more comprehensive fix is still pending)
** Fixed a number of minor bugs
** Some known bugs still exist
*** SKAT-O Lambda eigenvalue error. This happenes in a particular context but haven't nailed down a way to prevent it yet.
*** EMMAX has case and control frequency flipped.
* EMMAX test has a silly known bug with case / ctrl frequency is flipped
* March 25th, 2013 : EPACTS v3.2.3 release
* March 25th, 2013 : EPACTS v3.2.3 release
** Relaxed the checking of low-rank matrix in SKAT tests (to avoid unncessary skipping of genes)
** Relaxed the checking of low-rank matrix in SKAT tests (to avoid unncessary skipping of genes)
