Overview

clam is a command-line tool for population genomics that provides an efficient workflow for calculating accurate population genetic statistics. Instead of requiring an all-sites VCF (which can be prohibitively large), clam uses a two-step process:

1. First, identify genomic regions with sufficient sequencing depth to be considered "callable" using clam loci
2. Then, calculate population genetic statistics using these callable regions and a VCF containing variants with clam stat

This approach eliminates the need for generating all-sites VCF files while still producing accurate diversity estimates, making it particularly suitable for large population genomics datasets.