broadinstitute/gatk-sv

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

Long read based human genomic structural variation detection with cuteSV

Copy number variant detection from targeted DNA sequencing

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.

Structural variation caller using third generation sequencing

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

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

Official code repository for GATK versions 4 and up