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SeqShop: Genetic Association Analysis Practical, June 2014 (view source)

Revision as of 10:27, 2 February 2017

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→‎Download & Build EPACTS
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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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* 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
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== Setup in person at the SeqShop Workshop ==
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''This section is specifically for the SeqShop Workshop computers.''
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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''If you are not running during the SeqShop Workshop, please skip this section.''
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<div class="mw-collapsible-content">
    
{{SeqShopLogin}}
 
{{SeqShopLogin}}
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== Setup your run environment==
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=== Setup your run environment===
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This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
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This is a  setup similar to the Structural Variant session.
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This will setup some environment variables to point you to
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* [[GotCloud]] program
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* EPACTS software
   
* Tutorial input files
 
* Tutorial input files
 
* Setup an output directory
 
* Setup an output directory
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* 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
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** If you want to view the detail of the set up, type
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** If you want to view the detail of the setup, type
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  less /home/hmkang/seqshop/setup.txt
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  less /home/mktrost/seqshop/setup.txt
 
and press 'q' to finish.
 
and press 'q' to finish.
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<div class="mw-collapsible mw-collapsed" style="width:200px">
 
<div class="mw-collapsible mw-collapsed" style="width:200px">
 
View setup.txt
 
View setup.txt
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  export OUT=~/out
 
  export OUT=~/out
 
  mkdir -p ${OUT}
 
  mkdir -p ${OUT}
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</div>
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</div>
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</div>
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</div>
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== Setup when running on your own outside of the SeqShop Workshop ==
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''This section is specifically for running on your own outside of the SeqShop Workshop.''
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<div class="mw-collapsible" style="width:600px">
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''If you are running during the SeqShop Workshop, please skip this section.''
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<div class="mw-collapsible-content">
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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]]
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=== Download & Build EPACTS ===
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If you do not already have EPACTS:
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* cd to where you want EPACTS installed (you can change this to any directory you want)
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mkdir -p ~/seqshop
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cd ~/seqshop/
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* download, decompress, and build the version of epacts that was tested with this tutorial:
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wget http://csg.sph.umich.edu//kang/epacts/download/EPACTS-3.2.6.tar.gz
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tar xvf EPACTS-3.2.6.tar.gz
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cd EPACTS-3.2.6
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./configure --prefix=$HOME/seqshop/epacts
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make
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make install
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cd ../..
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{{SeqShopRemoteEnv}}
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<ul>
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<li> Additional variables for EPACTS:</li>
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<ul>
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<div class="mw-collapsible" style="width:500px">
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<li>Using bash (replace the paths below with the appropriate paths):</li>
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<div class="mw-collapsible-content">
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:<pre>export EPACTS=~/seqshop/epacts</pre>
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</div>
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</div>
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<div class="mw-collapsible mw-collapsed" style="width:500px">
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<li>Using tcsh (replace the paths below with the appropriate paths):</li>
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<div class="mw-collapsible-content">
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:<pre>setenv EPACTS ~/seqshop/epacts</pre>
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</div>
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</div>
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</ul>
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</ul>
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</div>
 
</div>
 
</div>
 
</div>
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  mkdir --p $OUT/assoc
 
  mkdir --p $OUT/assoc
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  $EPACTS/bin/epacts-anno --in $OUT/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out $OUT/assoc/snps.anno.vcf.gz
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  $EPACTS/bin/epacts-anno --in $OUT/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out $OUT/assoc/snps.anno.vcf.gz --ref $SS/ref22/human.g1k.v37.chr22.fa
    
Then you will see a series of messages before annotation finishes.
 
Then you will see a series of messages before annotation finishes.
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<div class="mw-collapsible-content" style="width:800px">
 
<div class="mw-collapsible-content" style="width:800px">
 
  /home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz -r \
 
  /home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz -r \
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     /home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz \
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     /home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa -f refGene -g /home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz \
 
   -c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o  /net/seqshop-server/hmkang/out/assoc/snps.anno.vcf.gz --inputFormat vcf \
 
   -c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o  /net/seqshop-server/hmkang/out/assoc/snps.anno.vcf.gz --inputFormat vcf \
 
   -p /home/hmkang/seqshop/epacts/share/EPACTS/priority.txt
 
   -p /home/hmkang/seqshop/epacts/share/EPACTS/priority.txt
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           Gene Annotation
 
           Gene Annotation
 
             Parameters : -g [/home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz]
 
             Parameters : -g [/home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz]
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                           -r [/home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta]
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                           -r [/home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa]
 
                           --inputFormat [vcf], --checkReference, -f [refGene]
 
                           --inputFormat [vcf], --checkReference, -f [refGene]
 
                           -p [/home/hmkang/seqshop/epacts/share/EPACTS/priority.txt]
 
                           -p [/home/hmkang/seqshop/epacts/share/EPACTS/priority.txt]
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                           -u [], -d [], --se [], --si [], --outputFormat []
 
                           -u [], -d [], --se [], --si [], --outputFormat []
 
   Other Annotation Tools : --genomeScore [], --bed [], --tabix []
 
   Other Annotation Tools : --genomeScore [], --bed [], --tabix []
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  Load reference genome /home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta...
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  Load reference genome /home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa...
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  DONE: 84 chromosomes and 3101804739 bases are loaded.
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  DONE: 1 chromosomes and 51304566 bases are loaded.
 
  Load codon file /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt...
 
  Load codon file /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt...
 
  DONE: codon file loaded.
 
  DONE: codon file loaded.
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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
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  $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  
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  $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
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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
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  $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
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  $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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</div>
 
</div>
 
</div>
 
</div>
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== FEEDBACK ==
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Thursday Feedback:
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https://docs.google.com/forms/d/19XLCNmU3orvsgNDkzMXgypg4Dy_nPdH1UsReBl2lUZs/viewform
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If you didn't provide feedback for Tuesday and Wednesday, you can still do that here:
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https://docs.google.com/forms/d/1qaLHq9w1Ib3FZq0CtlrbK_-breNiqGRV06oRYNmUuME/viewform
 
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