ksamuk/pixy

Tools test whether admixture occurred and more

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. This is a comprehensive update to it.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Bioinformatics program inStrain

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.