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Jump to navigationJump to searchTutorial: EMMAX GotCloud STOM: Lecture 8 (view source)
Revision as of 02:31, 7 January 2014
, 02:31, 7 January 2014→Lecture 8
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 ===
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 ===
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
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
* 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
