Changes

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.

To conserve time and disk-space, our analysis will focus on a small region on chromosome 20, 42900000 - 43200000. We will first map the reads for two individuals (HG00096, HG00100).  We will then combine the results with mapped reads from the other 58 individuals to generate a list of polymorphic sites and estimate accurate genotypes at each of these sites.

To conserve time and disk-space, our analysis will focus on a small region on chromosome 20, 42900000 - 43200000. We will first map the reads for two individuals (HG00096, HG00100).   

 

The 2nd step is to use the 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.tar

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

Upon successful completion of the variant calling pipeline, you will see the following message:  

Upon successful completion of the variant calling pipeline, you will see the following message:  

   Commands finished in xxx secs with no errors reported

   Commands finished in nnn secs with no errors reported

The final VCF produced by the variant calling pipeline containing only the variants that passed all filters is:

The final VCF produced by the variant calling pipeline containing only the variants that passed all filters is:

Upon successful completion of this pipeline, you will see the following message:  

Upon successful completion of this pipeline, you will see the following message:  

  Commands finished in xxx secs with no errors reported

  Commands finished in nnn secs with no errors reported

The output from the beagle step of the genotype refinement pipeline is found in:

The output from the beagle step of the genotype refinement pipeline is found in:

 

= Tutorial Inputs / Modifying the Tutorial Inputs to Run Your Own Data =

= Modifying the Tutorial Inputs to Run Your Own Data =

== Alignment Pipeline ==

== Alignment Pipeline ==

The inputs to the alignment pipeline are  

The inputs to the tutorial alignment pipeline are:

===Index file===

===Index file===