samtools/bcftools

Official code repository for GATK versions 4 and up

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

Tools (written in C using htslib) for manipulating next-generation sequencing data

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.

cython + htslib == fast VCF and BCF processing

tools for working with genome variation graphs

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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