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Revision as of 10:27, 2 February 2017
, 10:27, 2 February 2017→Download & Build EPACTS
'''Note:''' the latest version of this practical is available at: [[SeqShop: Genetic Association Analysis Practical]]
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
== 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]]
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 ===
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-3.2.5.tar.gz
wget http://csg.sph.umich.edu//kang/epacts/download/EPACTS-3.2.6.tar.gz
tar xvf EPACTS-3.2.5.tar.gz
tar xvf EPACTS-3.2.6.tar.gz
cd EPACTS-3.2.5
cd EPACTS-3.2.6
./configure --prefix=$HOME/seqshop/epacts
./configure --prefix=$HOME/seqshop/epacts
make
make
<li>Using bash (replace the paths below with the appropriate paths):</li>
<li>Using bash (replace the paths below with the appropriate paths):</li>
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:<pre>export EPACTS=$SS/epacts</pre>
:<pre>export EPACTS=~/seqshop/epacts</pre>
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<li>Using tcsh (replace the paths below with the appropriate paths):</li>
<li>Using tcsh (replace the paths below with the appropriate paths):</li>
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:<pre>setenv EPACTS $SS/epacts</pre>
:<pre>setenv EPACTS ~/seqshop/epacts</pre>
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== Preparing Input Files ==
== Preparing Input Files ==
If you want to run a collapsing burden test (CMC), run the following command
If you want to run a collapsing burden test (CMC), run the following command
$EPACTS/bin/epacts group --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.collapse --test b.collapse --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
$EPACTS/bin/epacts group --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.collapse --test b.collapse --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
You can view the results by examining the output file
You can view the results by examining the output file
You can run SKAT-O test in a similar way, but with a special tag
You can run SKAT-O test in a similar way, but with a special tag
$EPACTS/bin/epacts group --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.skato --test skat --skat-o --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
$EPACTS/bin/epacts group --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/group.skato --test skat --skat-o --groupf $OUT/assoc/snps.anno.grp --pheno PHENO --run 2
And view output files
And view output files
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