clam

clam identifies genomic regions with sufficient sequencing depth to be considered "callable" and uses this information to calculate population genetic statistics from VCFs. It eliminates the need to generate all-sites VCF files while still producing accurate diversity estimates.

clam was designed specifically for large population genomics datasets.

Installation

From bioconda:

conda create -n clam bioconda::clam

From source:

git clone https://github.com/cademirch/clam.git
cd clam
cargo build --release
./target/release/clam --help

Quick Start

1. Generate callable loci from depth data

clam loci -o callable.zarr -m 10 -t 8 *.d4.gz

2. Calculate population genetic statistics

clam stat -o results/ -w 10000 -c callable.zarr variants.vcf.gz

Commands

clam has three main commands:

Command	Description
`loci`	Generate callable loci from depth files (D4, GVCF)
`stat`	Calculate π, d_xy, F_ST, and heterozygosity from VCF using callable sites
`collect`	Pre-process depth files into Zarr for repeated use

Citation

If you use clam in your research, please cite:

Mirchandani C, Enbody E, Sackton TB, Corbett-Detig R. Efficient estimation of nucleotide diversity and divergence using callable loci (and more). Mol Biol Evol. 2025;msaf282. doi:10.1093/molbev/msaf282

@article{Mirchandani2025-hx,
  title     = {Efficient estimation of nucleotide diversity and divergence using
               callable loci (and more)},
  author    = {Mirchandani, Cade and Enbody, Erik and Sackton, Timothy B and
               Corbett-Detig, Russ},
  journal   = {Mol. Biol. Evol.},
  publisher = {Oxford University Press (OUP)},
  number    = {msaf282},
  month     = nov,
  year      = 2025,
  language  = {en}
}

License

clam is distributed under the terms of the MIT license.