pGermlinePoly is an software tool to separate true somatic mutations from germline variation in "clonal" sequencing datasets in the absence of a germline control sample. The underlying model uses external annotations (e.g., population allele frequency) to estimate a posterior probability of germline polymorphism. The model is released prior to a preprint for ease of inclusion in collaborative pipelines.
trace is a model to infer introgression using ancestral recombination graphs (ARGs) based on a model looking for distortions in local genealogies. It was co-developed with Yulin Zhang at UC Berkeley. If you use this method, please cite this preprint
karyoHMM is a model to infer chromosomal gains and losses from noisy array-based PGT-A datasets. The model is based on conditional distributions of B-allele frequencies from genotyping arrays. The version linked above is the development version of the software. If you use this package, please cite this paper
GeoVar is a software tool for coarse-grained visualization of multi-population patterns of allele sharing in python. If you use this package please cite this paper.
qtl-power is a python package that allows for easy calculation and plotting of power for genome-wide association studies (GWAS) under a number of experimental settings. Some features of this package are currently more experimental (e.g. burden-testing power estimation).
A small workflow I wrote while in industry to support automated QC of Olink targetted proteomics data for downstream applications.
A workflow for performing reference-based (and within sample) haplotype phasing using pre-existing software as a prior step to imputation.
A collection of plotting utilities and functions for matplotlib that I have accrued over the years. Most of the routines are inspired by having to remake plots for publication or common plots useful in statistical genetics.