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- 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:
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