Tutorial: GotCloud - Revision history

Mktrost at 16:35, 10 January 2014

2014-01-10T16:35:38Z

← Older revision		Revision as of 12:35, 10 January 2014
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	cd ~		cd ~
	wget https://github.com/statgen/gotcloud~~-latest~~/archive/latest.tar.gz # Download		wget https://github.com/statgen/gotcloud/archive/latest.tar.gz # Download
	tar xf latest.tar.gz # Extracts into gotcloud-latest/		tar xf latest.tar.gz # Extracts into gotcloud-latest/
	cd gotcloud-latest/src; make # Build source		cd gotcloud-latest/src; make # Build source

Mktrost at 22:24, 7 August 2013

2013-08-07T22:24:01Z

← Older revision		Revision as of 18:24, 7 August 2013
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	We will use 3 different directories for this tutorial:		We will use 3 different directories for this tutorial:
	# path to the directory where gotcloud is installed, default ~/gotcloud/		# path to the directory where gotcloud is installed, default ~/gotcloud-latest/
	# path to the directory where the example data is installed, default ~/gotcloudExample		# path to the directory where the example data is installed, default ~/gotcloudExample
	# path to your output directory, default ~/gotcloudTutorialOut/		# path to your output directory, default ~/gotcloudTutorialOut/
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	Otherwise, you can install it in your own directory:		Otherwise, you can install it in your own directory:
	# Change to the directory where you want gotcloud/ installed		# Change to the directory where you want gotcloud-latest/ installed
	# Download the gotcloud tar ~~from the ftp site~~.		# Download the gotcloud tar.
	# Extract the tar		# Extract the tar
	# Build (compile) the source		# Build (compile) the source
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	cd ~		cd ~
	wget https://github.com/statgen/gotcloud/archive/latest.tar.gz # Download		wget https://github.com/statgen/gotcloud-latest/archive/latest.tar.gz # Download
	tar xf latest.~~tgz~~ # Extracts into gotcloud/		tar xf latest.tar.gz # Extracts into gotcloud-latest/
	cd gotcloud-latest/src; make # Build source		cd gotcloud-latest/src; make # Build source

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	Run the variant calling pipeline:		Run the variant calling pipeline:
	cd ~		cd ~
	gotcloud/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample		gotcloud-latest/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample

	Upon successful completion of the variant calling pipeline (about 2-4 minutes), you will see the following message:		Upon successful completion of the variant calling pipeline (about 2-4 minutes), you will see the following message:
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	Run the LD-aware genotype refinement pipeline:		Run the LD-aware genotype refinement pipeline:
	cd ~		cd ~
	gotcloud/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample		gotcloud-latest/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample

	Upon successful completion of this pipeline (about 3-10 minutes), you will see the following message:		Upon successful completion of this pipeline (about 3-10 minutes), you will see the following message:

Mktrost: /* STEP 2 : Run GotCloud Alignment Pipeline */

2013-08-07T22:14:18Z

STEP 2 : Run GotCloud Alignment Pipeline

← Older revision		Revision as of 18:14, 7 August 2013
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	Run the alignment pipeline (the example aligns 2 samples) :		Run the alignment pipeline (the example aligns 2 samples) :
	cd ~		cd ~
	gotcloud/gotcloud align --conf gotcloudExample/[[#Alignment Configuration File\|GBR2align.conf]] --outdir [[#Alignment Output Directory\|gotcloudTutorialOut]] --baseprefix gotcloudExample		gotcloud-latest/gotcloud align --conf gotcloudExample/[[#Alignment Configuration File\|GBR2align.conf]] --outdir [[#Alignment Output Directory\|gotcloudTutorialOut]] --baseprefix gotcloudExample

	Upon successful completion of the alignment pipeline (about 1-3 minutes), you will see the following message:		Upon successful completion of the alignment pipeline (about 1-3 minutes), you will see the following message:

Mktrost: /* Step 1a: Install GotCloud */

2013-08-07T22:13:54Z

Step 1a: Install GotCloud

← Older revision		Revision as of 18:13, 7 August 2013
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	cd ~		cd ~
	wget ~~ftp~~://~~share~~.~~sph.umich.edu~~/gotcloud/~~gotcloud_latest~~.~~tgz~~ # Download		wget https://github.com/statgen/gotcloud/archive/latest.tar.gz # Download
	tar xf ~~gotcloud_latest~~.tgz # Extracts into gotcloud/		tar xf latest.tgz # Extracts into gotcloud/
	cd gotcloud/src; make # Build source		cd gotcloud-latest/src; make # Build source

	=== Step 1b: Install Example Dataset ===		=== Step 1b: Install Example Dataset ===

Mktrost: /* STEP 4 : Run GotCloud Genotype Refinement Pipeline */

2013-08-02T19:57:34Z

STEP 4 : Run GotCloud Genotype Refinement Pipeline

← Older revision		Revision as of 15:57, 2 August 2013
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	The output from the thunderVcf (final step) of the genotype refinement pipeline is found in:		The output from the thunderVcf (final step) of the genotype refinement pipeline is found in:
	ls gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi		ls gotcloudTutorialOut/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi

	== STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) ==		== STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) ==

Mktrost: /* STEP 4 : Run GotCloud Genotype Refinement Pipeline */

2013-08-02T19:56:25Z

STEP 4 : Run GotCloud Genotype Refinement Pipeline

← Older revision		Revision as of 15:56, 2 August 2013
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	gotcloud/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample		gotcloud/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample

	Upon successful completion of this pipeline (about 10 minutes), you will see the following message:		Upon successful completion of this pipeline (about 3-10 minutes), you will see the following message:
	Commands finished in nnn secs with no errors reported		Commands finished in nnn secs with no errors reported

Mktrost: /* STEP 4 : Run GotCloud Genotype Refinement Pipeline */

2013-08-02T19:21:35Z

STEP 4 : Run GotCloud Genotype Refinement Pipeline

← Older revision		Revision as of 15:21, 2 August 2013
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	Run the LD-aware genotype refinement pipeline:		Run the LD-aware genotype refinement pipeline:
	~/gotcloud/gotcloud ldrefine --conf ~/gotcloudExample/[[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2 --baseprefix ~/gotcloudExample		cd ~
			gotcloud/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample

	Upon successful completion of this pipeline (about 10 minutes), you will see the following message:		Upon successful completion of this pipeline (about 10 minutes), you will see the following message:
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	The output from the beagle step of the genotype refinement pipeline is found in:		The output from the beagle step of the genotype refinement pipeline is found in:
	ls ~/gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz ~/gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz.tbi		ls gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz.tbi

	The output from the thunderVcf (final step) of the genotype refinement pipeline is found in:		The output from the thunderVcf (final step) of the genotype refinement pipeline is found in:
	ls ~/gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz ~/gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi		ls gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi



	== STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) ==		== STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) ==

Mktrost: /* STEP 3 : Run GotCloud Variant Calling Pipeline */

2013-08-02T19:19:46Z

STEP 3 : Run GotCloud Variant Calling Pipeline

← Older revision		Revision as of 15:19, 2 August 2013
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	** chr20.merged.vcf.OK - indicator that the step completed successfully		** chr20.merged.vcf.OK - indicator that the step completed successfully
	* the hardfiltered (pre-svm filtered) variant calls:		* the hardfiltered (pre-svm filtered) variant calls:
	** chr20.~~filtered~~.vcf.gz - vcf for whole chromosome after it has been run through hard filters		** chr20.hardfiltered.vcf.gz - vcf for whole chromosome after it has been run through hard filters
	** chr20.hardfiltered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes		** chr20.hardfiltered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes
	** chr20.hardfiltered.sites.vcf.log - log file		** chr20.hardfiltered.sites.vcf.log - log file

Mktrost: /* STEP 3 : Run GotCloud Variant Calling Pipeline */

2013-08-02T19:18:11Z

STEP 3 : Run GotCloud Variant Calling Pipeline

← Older revision		Revision as of 15:18, 2 August 2013
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	gotcloud/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample		gotcloud/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample

	Upon successful completion of the variant calling pipeline (about 3-4 minutes), you will see the following message:		Upon successful completion of the variant calling pipeline (about 2-4 minutes), you will see the following message:
	Commands finished in nnn secs with no errors reported		Commands finished in nnn secs with no errors reported

Mktrost: /* STEP 3 : Run GotCloud Variant Calling Pipeline */

2013-08-02T19:14:47Z

STEP 3 : Run GotCloud Variant Calling Pipeline

← Older revision		Revision as of 15:14, 2 August 2013
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	Run the variant calling pipeline:		Run the variant calling pipeline:
	~/gotcloud/gotcloud snpcall --conf ~/gotcloudExample/[[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix ~/gotcloudExample		cd ~
			gotcloud/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample

	Upon successful completion of the variant calling pipeline (about 3-4 minutes), you will see the following message:		Upon successful completion of the variant calling pipeline (about 3-4 minutes), you will see the following message:
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	On SNP Call success, the VCF files of interest are:		On SNP Call success, the VCF files of interest are:
	ls ~/gotcloudTutorialOut/vcfs/chr20/chr20.filtered*		ls gotcloudTutorialOut/vcfs/chr20/chr20.filtered*

	This gives you the following files:		This gives you the following files:
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	Note: the tutorial does not produce a target directory, but if you run with targeted data, you may see that.		Note: the tutorial does not produce a target directory, but if you run with targeted data, you may see that.


	== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==		== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==