freebayes/freebayes

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

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Copy number variant detection from targeted DNA sequencing

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

Structural variation caller using third generation sequencing

Graph-based alignment (Hierarchical Graph FM index)

tools for working with genome variation graphs

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

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing