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#Download and install EPACTS
#Download and install EPACTS
#Convert the minimac or Impute2 output into VCF format
#Prepare VCF file with genotypes / dosages
#Prepre PED file for phenotypes and covariates
#Prepare PED file with phenotypes and covariates
#Run EPACTS association pipeline
#Run EPACTS association pipeline
#Report association results in appropriate format
#Report association results in appropriate format
== 1. Download and install EPACTS ==
== 1. Download and install EPACTS ==
=== For external Users ===
=== For external Users ===
For external users, follow the instruction at [[EPACTS]] page, summarized below.
*Download EPACTS binary at http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2.1.noref_binary.2012_07_03.tar.gz (101MB)
*Uncompress EPACTS package to the directory you would like to install
tar xzvf epacts_v2.1.noref_binary.2012_07_03.tar.gz
tar xzvf epacts_v2.1.noref_binary.2012_07_03.tar.gz
* Download the reference FASTA files by running the following commands
*Download the reference FASTA files by running the following commands
cd epacts2.1/
cd epacts2.1/
./ref_download.sh (Or copy the FASTA and index file locally you have to ${EPACTS_DIR}/ext/ref/)
* Perform a test run by running the following command
*Perform a test run by running the following command
example/test_run_epacts.sh
example/test_run_epacts.sh
=== For Local Users in CSG ===
=== For Local Users in CSG ===
For users in CSG, EPACTS can be found here:
For users in CSG, EPACTS can be found here:
<pre>/net/fantasia/home/hmkang/sw/epacts2.1/</pre>
<pre>/net/fantasia/home/hmkang/sw/epacts2.1/</pre>
--out {OUTPUT_DIR}/test --run 2 &
--out {OUTPUT_DIR}/test --run 2 &
</pre>
</pre>
This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001. The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX. The output file directory prefix is {OUTPUT_DIR}/test. Finally, EPACTS will run the analysis in parallel on 2 CPUs.
This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001. The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX. The output file directory prefix is {OUTPUT_DIR}/test. Finally, EPACTS will run the analysis in parallel on 2 CPUs.
== 2. Convert the minimac or Impute2 output into VCF format ==
== 2. Prepare VCF file with genotypes / dosages ==
EPACTS requires input genotype / doseage information in VCF format. After imputation with either minimac or Impute2, use this wrapper program "dose2vcf" to convert your doseage output to VCF format.
EPACTS requires input genotype / doseage information in VCF format. From minimac or Impute2, you wil start with your imputed dosage file.
=== A. Convert doseage file into VCF format ===
Use the wrapper program "dose2vcf" to convert your doseage output to VCF format. Download and install the wrapper program here. [ PLEASE COMPLETE ]
To run the wrapper program, use the following command
To run the wrapper program, use the following command
<pre>> dose2vcf/dose2vcf --dose FUSION.GWAS.1KG.imp.chr1.dose --info FUSION.GWAS.1KG.imp.chr1.info --out out/FUSION.GWAS.1KG.imp.chr1</pre>
<pre>> dose2vcf/dose2vcf --dose FUSION.GWAS.1KG.imp.chr1.dose --info FUSION.GWAS.1KG.imp.chr1.info --out out/FUSION.GWAS.1KG.imp.chr1</pre>
The expected output file is:
The expected output file is:
<pre>out/FUSION.GWAS.1KG.imp.chr1.vcf</pre>
<pre>out/FUSION.GWAS.1KG.imp.chr1.vcf</pre>
=== B. bgzip and tabix VCF files ===
Input VCF file must be bgzipped and tabixed before running association to allow efficient random access of the file. Below is an example command to conver plain VCF into bgzipped and tabixed VCF
<pre>bgzip input.vcf ## this command will produce input.vcf.gz
tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi
</pre>
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.<br>Sample IDs in the VCF file must be consistent to those from PED file
== 3. Prepare PED file for phenotypes and covariates ==
== 3. Prepare PED file for phenotypes and covariates ==
etc.
etc.
An example PED file with a header is as follows. Note that the header must start with a "#" symbol.
An example PED file with a header is as follows. Note that the header must start with a "#" symbol.
<pre>#FAM_ID IND_ID FAT_ID MOT_ID SEX DISEASE QT AGE
<pre>#FAM_ID IND_ID FAT_ID MOT_ID SEX DISEASE QT AGE
13281 NA12344 NA12347 NA12348 1 1 94.17 66.1
13281 NA12344 NA12347 NA12348 1 1 94.17 66.1
M QT
M QT
M AGE
M AGE
</pre>
</pre>
== 4. Run EPACTS association pipeline ==
== 4. Run EPACTS association pipeline ==
To run the Firth test as well, use:
To run the Firth test as well, use:
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
<pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -run 10
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -run 10
</pre>
</pre>
Note that the Firth bias-corrected test is more computationally intensive than the score test.
Note that the Firth bias-corrected test is more computationally intensive than the score test.
For detailed description of options, use:
For detailed description of options, use:
<pre>epacts2.1/epacts single -man
<pre>epacts2.1/epacts single -man
</pre>
</pre>
== 5. Report association results in appropriate format<br> ==
== 5. Report association results in appropriate format<br> ==
