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The variant calling pipeline generates an initial list of polymorphic sites and genotypes stored in a VCF file and then uses haplotype information to refine these genotypes in an updated VCF file.
The variant calling pipeline generates an initial list of polymorphic sites and genotypes stored in a VCF file and then uses haplotype information to refine these genotypes in an updated VCF file.
== STEP 1 : Install GotCloud ==
== STEP 1 : Setup GotCloud ==
=== Step 1a: Install GotCloud ===
In order to run this tutorial, you need to make sure you have GotCloud is installed on your system.
In order to run this tutorial, you need to make sure you have GotCloud is installed on your system.
If you have root and would like to install gotcloud on your system, follow: [[GotCloud#Install_GotCloud_Software| root access installation instructions]]
=== Example Dataset ===
Otherwise, you can install it in your own directory:
# Change directory to where you want to install gotcloud
# Download the gotcloud tar from TBD
# Extract the tar
# Build the source
cd ~ # Move to your home directory (or wherever you want to install)
wget TBD # Download
tar xvf gotcloud.tar # Extract
cd gotcloud/src; make # Build source
=== Step 1b: Install Example Dataset ===
Our dataset consists of 60 individuals from GBR sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.
Our dataset consists of 60 individuals from GBR sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.
The example dataset we'll be using is included in this tar-ball TBD.
The example dataset we'll be using is included in this tar-ball TBD.
# Change directory to where you want to install the example dataset
# Download the dataset tar from TBD
# Extract the tar
cd ~ # Move to your home directory (or wherever you want to install)
wget TBD # Download
tar xvf gotcloudExample.tar # Extract
=== Step 1c: Setup Enviornment for Testing ===
To facilitate running this tutorial, set environment variables:
* GCHOME to the path to the base directory of your gotcloud instalation
* GCDATA to the path to the base directory of the example data instalation
In the instructions below, we
First check your shell using:
ps -p $$ -ocomm=
For bash, sh:
export GCHOME=~/gotcloud/
export GCDATA=~/gcTutorial/
For csh, tcsh:
setenv GCHOME ~/gotcloud/
setenv GCDATA ~/gcTutorial/
== STEP 2 : Run GotCloud Alignment Pipeline ==
== STEP 2 : Run GotCloud Alignment Pipeline ==
Run the mapping pipeline:
Run the mapping pipeline:
gen_biopipeline.pl --conf [[GBR60map.conf]] --out_dir mappingResults
$GCHOME/gen_biopipeline.pl --conf $GCDATA/[[GBR60map.conf]] --out_dir mappingResults
TBD - add link explaining the contents of the .conf & .index files.
TBD - add link explaining the contents of the .conf & .index files.
== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==
== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==
Instructions for running Beagle/Thunder.
== STEP 5 : Run GotCloud Association Analysis Pipeline ==
== STEP 5 : Run GotCloud Association Analysis Pipeline ==
