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EPACTS for DIAGRAM (view source)

Revision as of 19:33, 1 December 2012

234 bytes removed ,  19:33, 1 December 2012
→‎1.  Download and install EPACTS
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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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*Download EPACTS binary at http://www.sph.umich.edu/csg/kang/epacts/download/epacts.v2.2.0.20121026.tar.gz (94MB)
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*http://www.sph.umich.edu/csg/kang/epacts/download/EPACTS-3.0.0.tar.gz (99MB)  
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*Uncompress EPACTS package to the directory you would like to install
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*Uncompress EPACTS package to the directory you would like to install and then type the following commands
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  tar xzvf epacts.v2.2.0.20121026.tar.gz
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>  tar xzvf EPACTS-3.0.0.tar.gz
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> cd EPACTS-3.0.0
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> ./configure --prefix [INSTALL DIRECTORY]
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> make
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> make install
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*Download the reference FASTA files from 1000 Genomes FTP automatically by running the following commands<br>
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<pre>cd epacts.v2.2.0.20121026/
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./ref_download.sh
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(For advanced users, to save time for downloading the FASTA files (~900MB), you may copy a local copy of GRCh37 FASTA file and the index file to ${EPACTS_DIR}/ext/ref/)
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</pre>
   
*Perform a test run by running the following command
 
*Perform a test run by running the following command
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</pre>  
 
</pre>  
 
<br> Run the single variant score test on the example data using this command:  
 
<br> Run the single variant score test on the example data using this command:  
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<pre>$ epacts.v2.2.0.20121026/epacts single  
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<pre>$ EPACTS-3.0.0/epacts single  
 
--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz  
 
--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz  
 
--ped epacts2.1/example/1000G_dummy_pheno.ped  
 
--ped epacts2.1/example/1000G_dummy_pheno.ped  
Clement Ma
216

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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/5970"

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