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EPACTS for DIAGRAM (view source)

Revision as of 13:34, 27 September 2012

649 bytes removed ,  13:34, 27 September 2012
→‎1.  Download and install EPACTS
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== 1.  Download and install EPACTS  ==
 
== 1.  Download and install EPACTS  ==
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EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here].
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=== For external Users ===
    
For external users, follow the instruction at [[EPACTS]] page, summarized below.
 
For external users, follow the instruction at [[EPACTS]] page, summarized below.
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   example/test_run_epacts.sh
 
   example/test_run_epacts.sh
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=== 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>  
 
<br> Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:  
 
<br> Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:  
 
<pre>$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
 
<pre>$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
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For external users, follow the instruction at [[EPACTS]] page, summarized below.
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* Download EPACTS binary at http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2.1.noref_binary.2012_07_03.tar.gz (94MB)
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* Uncompress EPACTS package to the directory you would like to install 
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  tar xzvf epacts_v2.1.noref_binary.2012_07_03.tar.gz
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* Download the reference FASTA files by running the following commands
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  cd epacts2.1/
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  ./ref_download.sh (Or copy the FASTA and index file locally you have to ${EPACTS_DIR}/ext/ref/)
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* Perform a test run by running the following command
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  example/test_run_epacts.sh
      
$ epacts2.1/example/1000G_dummy_pheno.ped
 
$ epacts2.1/example/1000G_dummy_pheno.ped
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/5327"

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