Difference between revisions of "Tutorial: EMMAX GotCloud STOM: Lecture 8"

From Genome Analysis Wiki
Jump to navigationJump to search
 
(5 intermediate revisions by the same user not shown)
Line 4: Line 4:
  
 
The slides describing the notes below are available [[Media:Stom practice 08.pdf | here (PDF)]]
 
The slides describing the notes below are available [[Media:Stom practice 08.pdf | here (PDF)]]
 +
 +
Updated version is available at https://www.dropbox.com/s/uhyjnqugovvbw6a/stom_practice_08.pdf 
  
 
=== Basic Setup ===
 
=== Basic Setup ===
Line 21: Line 23:
 
And use the VCF from practice 6 as the input  
 
And use the VCF from practice 6 as the input  
  
−
  ls $S5/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz
+
  ls ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz
  
 
=== Run Single Variant Analysis ===
 
=== Run Single Variant Analysis ===
Line 28: Line 30:
  
 
  mkdir ~/out/assoc
 
  mkdir ~/out/assoc
−
  $S5/epacts/bin/epacts single --ped $S5/examples/index/chr7.CFTR.ped --vcf $S5/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out ~/out/assoc/single.b.score --test b.score --anno --ref $S5/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
+
  $S5/epacts/bin/epacts single --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out ~/out/assoc/single.b.score --test b.score --anno --ref $S5/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
  
 
* Look at the association statistics
 
* Look at the association statistics
  
−
  head = ~/out/assoc/single.b.score.epacts.top5000
+
  head ~/out/assoc/single.b.score.epacts.top5000
  
 
* Variant annotation with EPACTS
 
* Variant annotation with EPACTS
Line 57: Line 59:
  
 
  cat ~/out/assoc/group.skat.o.epacts | cut -f 4,6,10,11
 
  cat ~/out/assoc/group.skat.o.epacts | cut -f 4,6,10,11
−
 
−
$S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.VT --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test VT --run 2
 
  
 
* Run Variable Threshold test
 
* Run Variable Threshold test
 
  $S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.VT --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test VT --run 2
 
  $S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.VT --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test VT --run 2
  
−
  * cat ~/out/assoc/group.VT.epacts | cut -f 4,6,10,13
+
  cat ~/out/assoc/group.VT.epacts | cut -f 4,6,10,13

Latest revision as of 02:31, 7 January 2014

STOM 2014 Workshop - Practical Sessions 8

Lecture 8

The slides describing the notes below are available here (PDF)

Updated version is available at https://www.dropbox.com/s/uhyjnqugovvbw6a/stom_practice_08.pdf

Basic Setup

  • Check if the files are still accessible
ls /data/stom2014/session5/
  • For convenience, let’s define environmental variable again
export S5=/data/stom2014/session5

Preparing Input Files

  • PED file - See the example provided
less $S5/examples/index/chr7.CFTR.ped

And use the VCF from practice 6 as the input 

ls ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz

Run Single Variant Analysis

  • Run score test
mkdir ~/out/assoc
$S5/epacts/bin/epacts single --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --pheno PHENO --out ~/out/assoc/single.b.score --test b.score --anno --ref $S5/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
  • Look at the association statistics
head ~/out/assoc/single.b.score.epacts.top5000
  • Variant annotation with EPACTS
$S5/epacts/bin/epacts anno --in ~/out/snps/beagle/chr7/chr7.filtered.PASS.beagled.vcf.gz --out ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --ref $S5/examples/chr7Ref/hs37d5.chr7.fa

Visualizing Zoom Plot

  • Use ENCODE GM12878 cell type to diplsy variants in the locusZoom-like plot
$S5/epacts/bin/epacts-zoom --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --pos 7:117149147 --prefix ~/out/assoc/single.b.score --cellType Gm12878

Copy the output file single.b.score.zoom.7.117149147.pdf using WinSCP or other file transfer software

Run Groupwise Test

  • Create a set of markers to test
$S5/epacts/bin/epacts make-group --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --nonsyn
  • Run SKAT-O test
$S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.skat.o --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test skat --skat-o --run 2

cat ~/out/assoc/group.skat.o.epacts | cut -f 4,6,10,11
  • Run Variable Threshold test
$S5/epacts/bin/epacts group --ped $S5/examples/index/chr7.CFTR.ped --vcf ~/out/snps/chr7.filtered.PASS.beagled.anno.vcf.gz --out ~/out/assoc/group.VT --groupf ~/out/snps/chr7.filtered.PASS.beagled.anno.grp --test VT --run 2

cat ~/out/assoc/group.VT.epacts | cut -f 4,6,10,13
Retrieved from "http://genome.sph.umich.edu/w/index.php?title=Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8&oldid=9328"