Changes

From Genome Analysis Wiki
Jump to navigationJump to search

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

Revision as of 10:27, 2 February 2017

2,176 bytes added ,  10:27, 2 February 2017
→‎Download & Build EPACTS
Line 1: Line 1:  +
'''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]]
   Line 9: Line 14:  
* 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.''
 +
<div class="mw-collapsible mw-collapsed" style="width:600px">
 +
''If you are not running during the SeqShop Workshop, please skip this section.''
 +
<div class="mw-collapsible-content">
    
{{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
Line 23: Line 34:  
* 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.
 +
 
<div class="mw-collapsible mw-collapsed" style="width:200px">
 
<div class="mw-collapsible mw-collapsed" style="width:200px">
 
View setup.txt
 
View setup.txt
Line 38: Line 50:  
  export OUT=~/out
 
  export OUT=~/out
 
  mkdir -p ${OUT}
 
  mkdir -p ${OUT}
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
 +
 +
== Setup when running on your own outside of the SeqShop Workshop ==
 +
''This section is specifically for running on your own outside of the SeqShop Workshop.''
 +
<div class="mw-collapsible" style="width:600px">
 +
''If you are running during the SeqShop Workshop, please skip this section.''
 +
<div class="mw-collapsible-content">
 +
 +
This tutorial builds on the alignment & snpcall tutorials, if you have not already, please first run those tutorials: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014|Alignment Tutorial]] & [[SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014|SNP Calling Tutorial]]
 +
 +
=== Download & Build EPACTS ===
 +
If you do not already have EPACTS:
 +
* cd to where you want EPACTS installed (you can change this to any directory you want)
 +
mkdir -p ~/seqshop
 +
cd ~/seqshop/
 +
* download, decompress, and build the version of epacts that was tested with this tutorial:
 +
wget http://csg.sph.umich.edu//kang/epacts/download/EPACTS-3.2.6.tar.gz
 +
tar xvf EPACTS-3.2.6.tar.gz
 +
cd EPACTS-3.2.6
 +
./configure --prefix=$HOME/seqshop/epacts
 +
make
 +
make install
 +
cd ../..
 +
 +
{{SeqShopRemoteEnv}}
 +
 +
<ul>
 +
<li> Additional variables for EPACTS:</li>
 +
<ul>
 +
<div class="mw-collapsible" style="width:500px">
 +
<li>Using bash (replace the paths below with the appropriate paths):</li>
 +
<div class="mw-collapsible-content">
 +
:<pre>export EPACTS=~/seqshop/epacts</pre>
 +
</div>
 +
</div>
 +
<div class="mw-collapsible mw-collapsed" style="width:500px">
 +
<li>Using tcsh (replace the paths below with the appropriate paths):</li>
 +
<div class="mw-collapsible-content">
 +
:<pre>setenv EPACTS ~/seqshop/epacts</pre>
 +
</div>
 +
</div>
 +
</ul>
 +
</ul>
 +
 
</div>
 
</div>
 
</div>
 
</div>
Line 103: Line 163:  
   
 
   
 
  mkdir --p $OUT/assoc
 
  mkdir --p $OUT/assoc
−
  $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
+
  $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.
Line 111: Line 171:  
<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 \
−
     /home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz \
+
     /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
Line 122: Line 182:  
           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]
−
                           -r [/home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta]
+
                           -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]
Line 128: Line 188:  
                           -u [], -d [], --se [], --si [], --outputFormat []
 
                           -u [], -d [], --se [], --si [], --outputFormat []
 
   Other Annotation Tools : --genomeScore [], --bed [], --tabix []
 
   Other Annotation Tools : --genomeScore [], --bed [], --tabix []
−
  Load reference genome /home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta...
+
  Load reference genome /home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa...
−
  DONE: 84 chromosomes and 3101804739 bases are loaded.
+
  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.
Line 191: Line 251:  
Let's run a single-variant association analysis using a score test.  
 
Let's run a single-variant association analysis using a score test.  
   −
  $EPACTS/bin/epacts-single --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --pheno PHENO --run 2  
+
  $EPACTS/bin/epacts-single --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --pheno PHENO --run 2  
    
After running it, you will see EPACTS output files by looking at
 
After running it, you will see EPACTS output files by looking at
Line 222: Line 282:  
View QQ plots
 
View QQ plots
 
<div class="mw-collapsible-content" style="width:800px">
 
<div class="mw-collapsible-content" style="width:800px">
 +
:<pre>evince $OUT/assoc/single.epacts.qq.pdf&</pre>
 
[[File:Single.epacts.qq.png]]
 
[[File:Single.epacts.qq.png]]
 
</div>
 
</div>
Line 229: Line 290:  
View Manhattan plots
 
View Manhattan plots
 
<div class="mw-collapsible-content" style="width:800px">
 
<div class="mw-collapsible-content" style="width:800px">
−
[[File:Single.epacts.mh.png]]
+
:<pre>evince $OUT/assoc/single.epacts.mh.pdf&</pre>
 +
[[File:Single.epacts.mh.png|900px]]
 
</div>
 
</div>
 
</div>
 
</div>
Line 240: Line 302:  
View Zoom Plots
 
View Zoom Plots
 
<div class="mw-collapsible-content" style="width:800px">
 
<div class="mw-collapsible-content" style="width:800px">
 +
:<pre>evince $OUT/assoc/single.zoom.22.36995620.pdf&</pre>
 
[[File:Single.zoom.22.36995620.png]]
 
[[File:Single.zoom.22.36995620.png]]
 
</div>
 
</div>
Line 250: Line 313:  
And run EMMAX test specifying the kinship matrix
 
And run EMMAX test specifying the kinship matrix
   −
  $EPACTS/bin/epacts-single --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/emmax --region 22:36000000-37000000 --test q.emmax --pheno PHENO --run 2 --kinf $OUT/assoc/snps.anno.kinf
+
  $EPACTS/bin/epacts-single --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/emmax --region 22:36000000-37000000 --test q.emmax --pheno PHENO --run 2 --kinf $OUT/assoc/snps.anno.kinf
    
Then the results may look similar to previous ones.
 
Then the results may look similar to previous ones.
    
  cat $OUT/assoc/emmax.epacts.top5000
 
  cat $OUT/assoc/emmax.epacts.top5000
−
      
== Run Groupwise Test ==
 
== Run Groupwise Test ==
Line 281: Line 343:  
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
Line 305: Line 367:  
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
Line 327: Line 389:  
</div>
 
</div>
 
</div>
 
</div>
−
  −
== FEEDBACK ==
  −
Thursday Feedback:
  −
  −
https://docs.google.com/forms/d/19XLCNmU3orvsgNDkzMXgypg4Dy_nPdH1UsReBl2lUZs/viewform
  −
  −
  −
If you didn't provide feedback for Tuesday and Wednesday, you can still do that here:
  −
  −
https://docs.google.com/forms/d/1qaLHq9w1Ib3FZq0CtlrbK_-breNiqGRV06oRYNmUuME/viewform
 
Ppwhite
96

edits

Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11116...14586"

Navigation menu