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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
** Fixed a number of minor bugs (more comprehensive fix is still pending)
* March 25th, 2013 : EPACTS v3.2.3 release
** Relaxed the checking of low-rank matrix in SKAT tests (to avoid unncessary skipping of genes)
* March 13th, 2013 : EPACTS v3.2.2 release
** Fixed an error which occasionally report mismatches in the number of samples
* March 9th, 2013 : EPACTS v3.2.1 release
* March 9th, 2013 : EPACTS v3.2.1 release
**Fixed errors in loading the dynamic library
**Fixed errors in loading the dynamic library
== 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.
== Currently Supported Statistical Tests ==
== Currently Supported Statistical Tests ==
| Implemented by
| Implemented by
|-
|-
| b.glm
| b.wald
| Binary
| Binary
| YES <br> (Joint)
| YES <br> (Joint)
| 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.
20 1616892 1616892 20:1616892_A/G_Synonymous:SIRPG 266 144 1 0.27068 0.0051239 2.7991 145 121 0.63449 0.42975
20 1616892 1616892 20:1616892_A/G_Synonymous:SIRPG 266 144 1 0.27068 0.0051239 2.7991 145 121 0.63449 0.42975
20 25038372 25038372 20:25038372_G/A_Intron:ACSS1 266 103.3 1 0.19418 0.005748 2.7618 145 121 0.47201 0.28813
20 25038372 25038372 20:25038372_G/A_Intron:ACSS1 266 103.3 1 0.19418 0.005748 2.7618 145 121 0.47201 0.28813
The key columns represents:
* '''NS''' : Number of phenotyped samples with non-missing genotypes
* '''AC''' : Total Non-reference Allele Count
* '''CALLRATE''' : Fraction of non-missing genotypes.
* '''MAF''' : Minor allele frequencies
* '''PVALUE''' : P-value of single variant test
* '''AF.CASE''' : Non-reference allele frequencies for cases
* '''AF.CTRL''' : Non-reference allele frequencies for controls
==== Q-Q plot of test statistics (stratified by MAF) ====
==== Q-Q plot of test statistics (stratified by MAF) ====
Note that [MARKER_ID_K] has to be sorted by increasing order of genomic coordinate
Note that [MARKER_ID_K] has to be sorted by increasing order of genomic coordinate
In oeder to create gene-level group file from typically formatted VCF file, one may use the following utility
In order to create gene-level group file from typically formatted VCF file, one may use the following utility
${EPACTS_DIR}/epacts make-group --vcf [input-vcf] --out [output-group-file] --format [epacts, annovar, chaos or gatk] --nonsyn
${EPACTS_DIR}/epacts make-group --vcf [input-vcf] --out [output-group-file] --format [epacts, annovar, chaos or gatk] --nonsyn
--groupf ${EPACTS_DIR}/data/1000G_exome_chr20_example_softFiltered.calls.anno.grp --out out/test.gene.skat \
--groupf ${EPACTS_DIR}/data/1000G_exome_chr20_example_softFiltered.calls.anno.grp --out out/test.gene.skat \
--ped ${EPACTS_DIR}/data/1000G_dummy_pheno.ped --maxAF 0.05 \
--ped ${EPACTS_DIR}/data/1000G_dummy_pheno.ped --maxAF 0.05 \
--chr 20 --pheno QT --cov AGE --cov SEX --test skat --ska-o --run 2
--chr 20 --pheno QT --cov AGE --cov SEX --test skat --skat-o --run 2
==== Example Output ====
==== Example Output ====
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.
# What is VCF?
# What is VCF?
#* VCF refers to Variant Call Format
#* VCF refers to Variant Call Format
#* See [[http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 | 1000 Genomes wiki page]] for the detailed description of VCF format
#* See [[http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 1000 Genomes wiki page]] for the detailed description of VCF format
# Should input VCF be compressed into certain format?
# Should input VCF be compressed into certain format?
#* Correct. EPACTS assumes that VCF file is bgzipped and tabixed already.
#* Correct. EPACTS assumes that VCF file is bgzipped and tabixed already.
#* [[#Manhattan Plot of Test Statistics]] will inform us the genome-wide distribution of association signals
#* [[#Manhattan Plot of Test Statistics]] will inform us the genome-wide distribution of association signals
#* [[#Output Text of All Test Statistics]] will contain the full information of test results across all units tested
#* [[#Output Text of All Test Statistics]] will contain the full information of test results across all units tested
# The Q-Q and Manhattan plots cannot be found. Why?
#* It is probably because gnuplot 4.2 or higher is not installed in your system, or they are included but cannot be found in your ${PATH}. Please visit [[http://gnuplot.info/ GNUPLOT web page]] for installation.
# 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.
$(EPACTS_DIR)/bin/pEmmax kin-util --kinf [input.kinf] --outf [output.prefix] --dump
=== More questions ===
=== More questions ===
# If you have more questions, please contact [[mailto:hmkang@umich.edu | Hyun Min Kang]].
# If you have more questions, please contact [[mailto:hmkang@umich.edu Hyun Min Kang]].
== Detailed Options ==
== Detailed Options ==
${EPACTS_DIR}/bin/epacts zoom -man (for zoom plot)
${EPACTS_DIR}/bin/epacts zoom -man (for zoom plot)
${EPACTS_DIR}/bin/epacts meta -man (for meta-analysis)
${EPACTS_DIR}/bin/epacts meta -man (for meta-analysis)
${EPACTS_DIR}/bin/epacts makegroup -man (for creating gene group)
${EPACTS_DIR}/bin/epacts make-group -man (for creating gene group)
== Implementing Additional Statistical Tests ==
== Implementing Additional Statistical Tests ==
== 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
** 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
** Relaxed the checking of low-rank matrix in SKAT tests (to avoid unncessary skipping of genes)
* March 13th, 2013 : EPACTS v3.2.2 release
** Fixed an error which occasionally report mismatches in the number of samples
* March 9th, 2013 : EPACTS v3.2.1 release
* March 9th, 2013 : EPACTS v3.2.1 release
**Fixed errors in loading the dynamic library
**Fixed errors in loading the dynamic library
