Segmented HAPlotype Estimation and Imputation Tool

Haplotype VCF comparison tools

Population-scale Ancestral Recombination Graph (ARG) library

The next version of bwa-mem

R's data.table package extends data.frame:

Segmented HAPlotype Estimation and Imputation Tool

Fast, accurate and simple to use command line tool for variant detection in NGS data.

simple jobs submission via command-line for AWS batch

Dropbear SSH

Deprecated. See new version: https://github.com/statgen/bravo_api - BRowse All Variants Online

A utility for merging and genotyping Illumina-style GVCFs.

A Fast Implementation of Random Forests

The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++

Bayesian haplotype-based mutation calling

A complete tool set for molecular QTL discovery and analysis

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead

Haplotype phasing software

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. This is a comprehensive upd…

Ancestry and Kinship Tools

Flexible genotype query among 30,000+ samples whole-genome

A flexible framework for rapid genome analysis and interpretation

gvcf aggregation tool

A single molecule sequence assembler for genomes large and small.

Comparisons of simulators for the msprime paper

This repo is DEPRECATED. Please use minimap2, the successor of minimap.

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

variant integration methods for the 1000 Genomes Project

Streaming algorithm for computing kmer statistics for massive genomics datasets

Aligner for sequencing data