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'''Note:''' the latest version of this practical is available at: [[SeqShop: Genetic Association Analysis Practical]]
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* The ones here is the original one from the June workshop (updated to be run from elsewhere)
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== Introduction ==
 
[[Media:Seqshop association 2014 06.pdf|View Lecture Slides]]
 
[[Media:Seqshop association 2014 06.pdf|View Lecture Slides]]
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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]]
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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, June 2014|Alignment Tutorial]] & [[SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014|SNP Calling Tutorial]]
    
=== Download & Build EPACTS ===
 
=== Download & Build EPACTS ===
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  cd ~/seqshop/
 
  cd ~/seqshop/
 
* download, decompress, and build the version of epacts that was tested with this tutorial:
 
* 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-3.2.6.tar.gz
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  wget http://csg.sph.umich.edu//kang/epacts/download/EPACTS-3.2.6.tar.gz
 
  tar xvf EPACTS-3.2.6.tar.gz
 
  tar xvf EPACTS-3.2.6.tar.gz
 
  cd EPACTS-3.2.6
 
  cd EPACTS-3.2.6
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