Tutorial: EMMAX GotCloud STOM: Lecture 8 - Revision history

Hmkang: /* Lecture 8 */

2014-01-07T06:31:12Z

Lecture 8

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	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 ===

2014-01-07T06:26:02Z

Run Groupwise Test

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	$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

2014-01-07T06:25:29Z

Run Groupwise Test

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	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

2014-01-07T06:21:32Z

Run Single Variant Analysis

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	* 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

2014-01-07T06:20:51Z

Run Single Variant Analysis

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	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

2014-01-07T06:19:28Z

Preparing Input Files

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	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 ===

2014-01-07T05:33:49Z

Run Groupwise Test

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	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		$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

2014-01-07T05:33:34Z

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	$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 $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

	* Look at ~~your score~~		* Look at the association statistics

	head = ~/out/assoc/single.b.score.epacts.top5000		head = ~/out/assoc/single.b.score.epacts.top5000

2014-01-07T05:14:14Z

Visualizing Zoom Plot =

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	$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		$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 ====		=== Visualizing Zoom Plot ===

	* Use ENCODE GM12878 cell type to diplsy variants in the locusZoom-like plot		* Use ENCODE GM12878 cell type to diplsy variants in the locusZoom-like plot

2014-01-07T00:00:11Z

Run Single Variant Analysis

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	* Look at your score		* Look at your score

	head = ~/out/assoc/single.b.score.epacts.~~top5000�~~		head = ~/out/assoc/single.b.score.epacts.top5000

	* Variant annotation with EPACTS		* 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		$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 ===		=== Run Groupwise Test ===