Using FreeBayes to call variants
The program FreeBayes can be used to call variants in genomes of any ploidy, pooled samples, or mixed populations.
Installation
This tutorial assumes that you have created the paths $WORK/src and $HOME/local/bin and added $HOME/local/bin to your {$PATH}.
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$ module load gcc login1$ make login1$ mv bin/* $HOME/local/bin
This command from the 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 created the executables inside of the source tree, so we can find and move them to our standard $HOME/local/bin directory.
Mixed population
Use 20K mixed population data from LTEE.