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.
- FreeBayes can be used to call variants in genomes of any ploidy, pooled samples, or mixed populations. It can be used on single samples.
- 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 $PATH
. FreeBayes uses a git repository and requires the cmake build system to compile. You can install it with these commands:
login1$ 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 $PATH where we have installed R 2.15:
export PATH="/corral-repl/utexas/BioITeam/ngs_course/local/bin:$PATH"
If you want to go through installing R 2.15 and deepSNV for yourself, here's how:
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