uterald

brca-pipeline

clinvar

Parsing ClinVar data

hgvs

HGVS variant name parsing and generation

jvarkit

Java utilities for Bioinformatics

sambamba

Tools for working with SAM/BAM data

svsim

Simulation toolbox for structural variations. (forked for package install)

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

yoruba

Query and modify BAM file contents; provides functions missing from some other tools