Difference between revisions of "Tutorial: EMMAX GotCloud STOM"

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= STOM 2014 Workshop - Practical Sessions =
 
= STOM 2014 Workshop - Practical Sessions =
  
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Welcome to Hyun Min Kang's practical session guide page for STOM 2014 workshop. If you do not know what STOM 2014 workshop is please follow the [[ http://bibs.snu.ac.kr/board/index.php?catid=201&bcid=344 | link]]
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Welcome to Hyun Min Kang's practical session guide page for STOM 2014 workshop. If you do not know what STOM 2014 workshop is please follow http://bibs.snu.ac.kr/board/index.php?catid=201&bcid=344
  
 
This page is intended to supplement the slides presented in the practical sessions of STOM 2014 workshop by facilitating easy copy-and paste of commands illustrated in the example, in the case the speed of the lecture is too fast for you.
 
This page is intended to supplement the slides presented in the practical sessions of STOM 2014 workshop by facilitating easy copy-and paste of commands illustrated in the example, in the case the speed of the lecture is too fast for you.
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Note that some commands can be very long and may go farther than the browser's width
 
Note that some commands can be very long and may go farther than the browser's width
  
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== Lecture 2 ==
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== Lecture 2 : Genomic Control, PCA, EMMAX ==
  
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* To see the files for the session, type
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_2 | Page for Practice 2 ]]
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ls /data/stom2014/session2/
 
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If you see any errors, please let me know now!
 
  
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* For convenience, let’s set some variables
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== Lecture 5 : GotCloud Alignment Pipeline ==
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  export S2=/data/stom2014/session2
 
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mkdir ~/out
 
  
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* Run naive association test using PLINK
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_5 | Page for Practice 5 ]]
  
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$S2/bin/plink --noweb --bfile $S2/data/1000G.auto.omni.phased.EUR --pheno $S2/data/1000G_EUR_20_1459060.phe --linear --out ~/out/naive
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== Lecture 6 : GotCloud Variant Calling Pipeline + samtools ==
  
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* Check your output file and see what it looks like
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_6 | Page for Practice 6 ]]
  
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less ~/out/naive.assoc.linear
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== Lecture 8 : Sequence-based association using EPACTS ==
  
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* Check the p-value at the causal variant
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8 | Page for Practice 8 ]]
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grep -w ADD ~/out/naive.assoc.linear | grep 20:1459060
 
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* Draw QQ plot using the following R commands
 
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> source('/data/stom2014/session2/r/qqconf.r')
 
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> T <- read.table('~/out/naive.assoc.linear',header=TRUE)
 
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> pdf('~/out/naive.pdf')
 
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> qq.conf.beta(T$P)
 
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> dev.off()
 
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* Add --adjust option to enable genomic control
 
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$S2/bin/plink --noweb --bfile $S2/data/1000G.auto.omni.phased.EUR --pheno $S2/data/1000G_EUR_20_1459060.phe --linear --adjust --out ~/out/naive
 
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* Calculate inflation factor on your own
 
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> T <- read.table('~/out/naive.assoc.linear',header=TRUE)
 
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** First, find the median p-value
 
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> median(T$P)
 
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> 0.4814
 
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** Convert p-value into chi-square using R, and compute lambda
 
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> qchisq(0.4814,1,lower.tail=FALSE)
 
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[1] 0,4956901
 
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> 0.4958032/0.456
 
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[1] 1.08704
 

Latest revision as of 10:56, 6 January 2014

STOM 2014 Workshop - Practical Sessions

Welcome to Hyun Min Kang's practical session guide page for STOM 2014 workshop. If you do not know what STOM 2014 workshop is please follow http://bibs.snu.ac.kr/board/index.php?catid=201&bcid=344

This page is intended to supplement the slides presented in the practical sessions of STOM 2014 workshop by facilitating easy copy-and paste of commands illustrated in the example, in the case the speed of the lecture is too fast for you.

This page only covers lecture 2, 5, 6, 8 that are taught by Hyun Min Kang.

Here I assume that

  • The audience has basic knowledge of Unix system, basic utilities, and pipes
  • The audience has the account in the cluster system and know how to access to the resources presented here

Note that some commands can be very long and may go farther than the browser's width

Lecture 2 : Genomic Control, PCA, EMMAX

Please see Page for Practice 2

Lecture 5 : GotCloud Alignment Pipeline

Please see Page for Practice 5

Lecture 6 : GotCloud Variant Calling Pipeline + samtools

Please see Page for Practice 6

Lecture 8 : Sequence-based association using EPACTS

Please see Page for Practice 8

Retrieved from "http://genome.sph.umich.edu/w/index.php?title=Tutorial:_EMMAX_GotCloud_STOM&oldid=9270"