Figure 4.

Code sample for the simple genotyper walker. The map function uses a naïve Bayesian method to generate genotypes, given the pileup of reference bases at the current locus, and emits a call containing the likelihoods for each of the 10 possible genotypes (assuming a diploid organism). This is then output to disk. The implementation of the tree-reduce function provides directions to the GATK engine for reducing two in-order parallel reduce results, allowing parallelization of the genotyper.