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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 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
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 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:
