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Genome variation in mixed samples (FreeBayes, deepSNV)

Genome variation in mixed samples (FreeBayes, deepSNV)

In this tutorial we will use two different programs to identify variants in mixed genomic samples where DNA from many individuals was pooled and sequenced together.

  1. FreeBayes can be used to call variants in genomes of any ploidy, pooled samples, or mixed populations. It can be used on single samples.
  2. deepSNV can be used to call single-nucleotide variants and single-base deletions in ultra-deep sequencing data sets. It compares variation between two samples.

Install FreeBayes

This tutorial assumes that you have created the paths $WORK/src and $HOME/local/bin and added $HOME/local/bin to your $PATH. FreeBayes uses a git repository and requires the cmake build system to compile. You can install it with these commands:

Installing FreeBayes from source
login1$ module load git
login1$ mkdir -p $WORK/src && cd $WORK/src
login1$ git clone --recursive git://github.com/ekg/freebayes.git
login1$ cd freebayes
login1$ module load cmake
login1$ make
login1$ mv bin/* $HOME/local/bin

This command from the FreeBayes instructions attempts to install to a system-wide location as super-user:

sudo make install

This won't work on Lonestar! (You aren't an admin.) However, the make command already created the executables inside of the bin directory in the source tree, so we can find and move them to our standard $HOME/local/bin directory with the last command.

Install deepSNV

The newest version of R on lonestar is currently 2.14, but deepSNV requires R version 2.15.

You can install your own version of R 2.15 on TACC using the instructions below, but this takes a while to compile, so you can also just add a location to your $PATH where we have installed R 2.15:

Using the copy of R 2.15 that we have already installed
export PATH="/corral-repl/utexas/BioITeam/ngs_course/local/bin:$PATH"

If you want to go through installing R 2.15 and deepSNV for yourself, here's how:

Installing R v2.15 from source in your
login1$ wget http://cran.wustl.edu/src/base/R-2/R-2.15.0.tar.gz
login1$ tar -xvzf R-2.15.0.tar.gz
login1$ cd R-2.15.0
login1$ ./configure --prefix=$HOME/local
login1$ make
login1$ make install

Once you have access to R 2.15, you can install deepSNV using these commands (which work for any BioConductor