Bioinformatics

Bioinformatics support on several studies and software development efforts related to statistical genetics, with a focus on human genomics and relationship inference.

Python package for probabilistic VCF genotype error simulation

R package with utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The ‘skater’ package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) ‘skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation’ doi:10.¹¹⁰¹⁄₂₀₂₁.07.21.453083.

Docker image to calculate non-reference concordance of SNP genotype calls in VCF file

some simple recipes for vcf data manipulation with bcftools

LOLAweb is a Shiny web server and interactive results viewer for enrichment of overlap between a query region set (a bed file) and a database of region sets. It provides an interactive result explorer to visualize the highest ranked enrichments from the database. You can access the web server at http://lolaweb.databio.org