GATK

Deep learning-based variant caller

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Bayesian haplotype-based polymorphism discovery and genotyping.

A C++ library for parsing and manipulating VCF files.

A polymorphic bayesian genotyping model with wide applicability.

Nallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly, and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional consequences.