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* Understand how to run rare variant association test using EPACTS
* Understand how to run rare variant association test using EPACTS
* Understand how to visualize the association output from EPACTS
* Understand how to visualize the association output from EPACTS
== Setup in person at the SeqShop Workshop ==
''This section is specifically for the SeqShop Workshop computers.''
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''If you are not running during the SeqShop Workshop, please skip this section.''
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{{SeqShopLogin}}
{{SeqShopLogin}}
== Setup your run environment==
=== Setup your run environment===
This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
This is a setup similar to the Structural Variant session.
This will setup some environment variables to point you to
* [[GotCloud]] program
* EPACTS software
* Tutorial input files
* Tutorial input files
* Setup an output directory
* Setup an output directory
* You won't see any output after running <code>source</code>
* You won't see any output after running <code>source</code>
** It silently sets up your environment
** It silently sets up your environment
** If you want to view the detail of the set up, type
** If you want to view the detail of the setup, type
less /home/hmkang/seqshop/setup.txt
less /home/mktrost/seqshop/setup.txt
and press 'q' to finish.
and press 'q' to finish.
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View setup.txt
View setup.txt
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== Setup when running on your own outside of the SeqShop Workshop ==
''This section is specifically for running on your own outside of the SeqShop Workshop.''
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''If you are running during the SeqShop Workshop, please skip this section.''
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This tutorial builds on the alignment & snpcall tutorials, if you have not already, please first run those tutorials: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] & [[SeqShop: Variant Calling and Filtering for SNPs Practical|SNP Calling Tutorial]]
=== Download & Build EPACTS ===
If you do not already have EPACTS:
* cd to where you want EPACTS installed (you can change this to any directory you want)
mkdir -p ~/seqshop
cd ~/seqshop/
* download, decompress, and build the version of epacts that was tested with this tutorial:
wget http://www.sph.umich.edu/csg/kang/epacts/download/EPACTS-3.2.5.tar.gz
tar xvf EPACTS-3.2.5.tar.gz
cd EPACTS-3.2.5
./configure --prefix=$HOME/seqshop/epacts
make
make install
cd ../..
{{SeqShopRemoteEnv}}
<ul>
<li> Additional variables for EPACTS:</li>
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<li>Using bash (replace the paths below with the appropriate paths):</li>
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:<pre>export EPACTS=$SS/epacts</pre>
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<li>Using tcsh (replace the paths below with the appropriate paths):</li>
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:<pre>setenv EPACTS $SS/epacts</pre>
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</ul>
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== Preparing Input Files ==
== Preparing Input Files ==
