teaguesterling/plinking_duck v0.1.0

v0.1.0 — Initial release

on GitHub

PlinkingDuck: a DuckDB extension for reading PLINK 2 genomics file formats and running common genetic analyses directly in SQL.

Documentation · Getting Started · Tutorial

What's Included

File readers:

• read_pvar — variant metadata (.pvar/.bim)
• read_psam — sample metadata (.psam/.fam)
• read_pgen — binary genotypes (.pgen)
• read_pfile — unified fileset reader with tidy mode

Analysis functions:

• plink_freq — per-variant allele frequencies
• plink_hardy — Hardy-Weinberg equilibrium exact test
• plink_missing — per-variant and per-sample missingness rates
• plink_ld — pairwise linkage disequilibrium (r², D, D')
• plink_score — polygenic risk scoring

Features

• Projection pushdown (skip genotype decompression for metadata queries)
• Parallel scan with atomic batch claiming
• Sample subsetting (by IID or index)
• Region filtering (chr:start-end)
• Variant filtering (by ID or index)
• Legacy PLINK 1 format support (.bim/.fam auto-detection)

Platform Support

• Linux amd64
• Linux arm64

Building

git clone --recurse-submodules https://github.com/teaguesterling/plinking_duck
cd plinking_duck
make