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