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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) |
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| == 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. |
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| | 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 |
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| | 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.score
| |
− | | Quantitative
| |
− | | YES <br> (Regressed Out)
| |
− | | Fast
| |
− | | Quantitative Score Test <br> (from Lin DY and Tang ZZ, AJHG 2011 89:354-67)
| |
− | | Clement Ma
| |
| |- | | |- |
| | q.linear | | | q.linear |
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| 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 |
| | | |
− | *Download EPACTS source distribution at http://www.sph.umich.edu/csg/kang/epacts/download/EPACTS-3.2.4.tar.gz (100MB)
| + | $ git clone https://github.com/statgen/EPACTS.git |
− | *Uncompress EPACTS package, and install the package using the following set of commands
| + | $ cd EPACTS |
| + | $ ./configure --prefix [/path/to/install] |
| + | $ make |
| + | $ make install |
| | | |
− | tar xzvf EPACTS-3.2.3.tar.gz
| |
− | cd EPACTS-3.2.3
| |
− | ./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) |
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| 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. |
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| 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. |
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| # How can I read the EMMAX kinship file from produced from EPACTS? | | # How can I read the EMMAX kinship file from produced from EPACTS? |
| # * You can run the following command to dump your kinship matrix into a human-readable text format. | | # * You can run the following command to dump your kinship matrix into a human-readable text format. |
− | $(EPACTS_DIR)/bin/epacts/bin/pEmmax kin-util --kinf [input.kinf] --outf [output.prefix] --dump | + | $(EPACTS_DIR)/bin/pEmmax kin-util --kinf [input.kinf] --outf [output.prefix] --dump |
| | | |
| === More questions === | | === More questions === |
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| | | |
| == 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 | | ** Fixed a number of minor bugs |