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 an all-sites VCF files while still producing accurate diversity estimates. clam was designed specifically for large population genomics datasets.
Installation
From bioconda:
From source:
git clone https://github.com/cademirch/clam.git
cd clam
cargo build --release
./target/release/clam --help
Basic Use
Generating callable loci intervals
The clam loci command can be used to generate callable loci intervals from sequencing depth data from either alignments or GVCF files. The resulting interval file describes how many samples were callable at each position in the genome.
Using callable loci intervals to estimate popgen statistics
The clam stat command can be used to estimate common population genetic statistics such as π, dxy, and FST in windows. stat uses the callable loci interval file alongside a VCF to produce accurate estimates, even in the presence of missing data.
Documentation
Read the documentation for more information.
License
clam is distributed under the terms of the MIT license.