Tutorial: EMMAX GotCloud STOM: Lecture 8

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