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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/
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
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 ===
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:
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:
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 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 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) ==
