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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 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.tar.gz # Extracts into gotcloud-latest/ |
− | cd gotcloud/src; make # Build source | + | cd gotcloud-latest/src; make # Build source |
| | | |
| === Step 1b: Install Example Dataset === | | === Step 1b: Install Example Dataset === |
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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: |
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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: |
− | ~/gotcloud/gotcloud ldrefine --conf ~/gotcloudExample/[[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2 --baseprefix ~/gotcloudExample | + | cd ~ |
| + | gotcloud-latest/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 |
| | | |
| 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/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi |
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− | | |
| | | |
| == STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) == | | == STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) == |