Tutorial: EMMAX GotCloud STOM: Lecture 8

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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