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freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

gatk-sv

gene_lists

List of gene lists for genomic analyses.

genomelink-python

Genomelink Python SDK

ggplot2-book

ggplot2: elegant graphics for data analysis

giggle

Interval data structure

gnomad_browser

tasks for ExAC + gnomad integration pre-ASHG

gsp_tools

Aggregation of tools developed by the Genome Sequencing Program. See the wiki.

hadoopcnv

HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data

hail

Scalable genomic data analysis.

hello-world

hemomips

Automated analysis and result reporting for targeted sequencing data

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

hpo_similarity

Analysis of similarity of HPO terms in groups of individuals

igv_utils

utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.

just-the-docs

A modern, high customizable, responsive Jekyll theme for documention with built-in search.

knitr

A general-purpose tool for dynamic report generation in R

linsight

loftee

long-read-validation

Long-read validation of BEDPE structural variation

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

manta

Structural variant and indel caller for mapped sequencing data

mergesvcallers

heuristics to merge structural variant calls in VCF format.

minigraph

Proof-of-concept seq-to-graph mapper and graph generator

mip_paper_2020

Custom code used in Wang et al. Nat Commun, 2020 (PMID: 33004838)

mipgen

One stop MIP design and analysis

mobster

Pair and mob programming timer for Mac, Windows, and Linux.

modern-unix

A collection of modern/faster/saner alternatives to common unix commands.

modules

Environment Modules: provides dynamic modification of a user's environment

mupit

De novo mutation recurrence significance testing