Changes

=== Step 1b: Install Example Dataset ===

=== Step 1b: Install Example Dataset ===

Our dataset consists of 60 individuals from Great Britain (GBR) sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.

Our dataset consists of individuals from Great Britain (GBR) sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.

To conserve time and disk-space, our analysis will focus on a small region on chromosome 20, 42900000 - 43200000.  

To conserve time and disk-space, our analysis will focus on a small region on chromosome 20, 42900000 - 43200000.  

The tutorial will run the alignment pipeline on 2 of the individuals (HG00096, HG00100).  The fastqs used for this step are reduced to reads that fall into our target region.

The alignment pipeline in this tutorial will be run on 2 of the individuals (HG00096, HG00100).  The fastqs used for this step are reduced to reads that fall into our target region.

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 snpcall and ldrefine pipelines will use previously aligned/mapped reads for 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.tgz  

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