In this section, we'll use a set of synthetic reads on the first 83 KB or so of the human genome chromosome 17. The reads were generated using the wgsim tool in samtools—an external command-line program. They have 64 SNPs introduced by wgsim, which can be seen in the sample data in datasets/ch2/snp_positions.txt. You'll see, as the program progresses, that by default the parameters find many more SNPs than there are—you'll need to spot the places where you can set the parameters properly to finely tune the SNP-finding process.