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  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:

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