bedtools - the swiss army knife for genome arithmetic

Toolset for SV simulation, comparison and filtering

Structural variant toolkit for VCFs

Jasmine: SV Merging Across Samples

Combine structural variation outputs from long sequencing reads into a superior call set

SV clustering

Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures.

RTG Tools: Utilities for accurate VCF comparison and manipulation

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Haplotype VCF comparison tools

Tools for the analysis of structural variation in genomes

robust matching of small variant datasets using flexible scoring schemes

A python wrapper around SURVIVOR

Tools to work with GWAS-VCF summary statistics files

Merging, Annotation, Validation, and Illustration of Structural variants