Population-scale genotyping using pangenome graphs

tools for genetic genealogy and the analysis of consumer DNA test results

Rare variant test software for next generation sequencing data

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Bayesian genotyper for structural variants

mgatk: mitochondrial genome analysis toolkit

Framework for Interpretable Neural Networks

PLINK reader for Python.

A Python package for pharmacogenomics (PGx) research

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Support Vector Structural Variation Genotyper

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

all methods related to Enterobase

SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.

This python script detects known traits in raw human genetic data.

GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for computational biology and genetics research.

Phasing and genotype Imputation comparison. Have been evaluated: BEAGLE 5.4, EAGLE 2.4.1, SHAPEIT 4, MINIMAC 4, IMPUTE 5, using accuracy metrics like: IQS(Imputation Quality score), r2 (Pearson correlation), Concordance.

A bioinformatics pipeline to phase and impute genetic data

Efficient compression and retrieve of genotype data with integer sparse matrices