GATK

Deep learning-based variant caller

samtools/bcftools are a suite of tools for manipulating NGS data and can be used to call variants.

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.