Changes

The tutorial will then used previously aligned/mapped reads for the full 60 individuals to generate a list of polymorphic sites and estimate accurate genotypes at each of these sites.  

The tutorial will then used previously aligned/mapped reads for the full 60 individuals to generate a list of polymorphic sites and estimate accurate genotypes at each of these sites.  

The example dataset we'll be using is available at: ftp://share.sph.umich.edu/gotcloud/gotcloudExample.tar

The example dataset we'll be using is available at: ftp://share.sph.umich.edu/gotcloud/gotcloudExample.tgz

# Create & Change directory to where you want to install the Tutorail data  

# Create & Change directory to where you want to install the Tutorail data  

  mkdir -p $GCDATA; cd $GCDATA  

  mkdir -p $GCDATA; cd $GCDATA  

  wget ftp://share.sph.umich.edu/gotcloud/gotcloudExample.tar.gz # Download  

  wget ftp://share.sph.umich.edu/gotcloud/gotcloudExample.tgz # Download  

  tar xvf gotcloudExample.tar.gz --strip 1  # Extract

  tar xvf gotcloudExample.tgz --strip 1  # Extract

== STEP 2 : Run GotCloud Alignment Pipeline ==  

== STEP 2 : Run GotCloud Alignment Pipeline ==