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 find and move them to our standard $HOME/local/bin directory with the last command.
Example 1: Mixed E. coli population
A mixed population of E. coli from an evolution experiment was sequenced at several different time points (PMID:19776167).
Data
The data for this example are in the path:
/corral-repl/utexas/BioITeam/ngs_course/FreeBayes/ecoli_mixed
File Name |
Description |
|---|---|
|
Illumina reads, 20K generation mixed population |
|
Illumina reads, 40K generation mixed population |
|
E. coli B str. REL606 genome |
The read files were downloaded from the ENA SRA study.
The reference genome file was downloaded from the NCBI Genomes page
Map Reads
Choose an appropriate program, map the reads, and convert the mapped reads to BAM format.