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clinvar

This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.

cromwell_intro

Dockerfile and wdl script for a simple cromwell / firecloud workflow

dbass

Database of de novo and cryptic splice site variants

elasticsearch-kubernetes-cluster

Scripts for deploying a stand-alone elasticsearch cluster - based on https://github.com/pires/kubernetes-elasticsearch-cluster

exac-readviz

Scripts used to generate the reassembled HaplotypeCaller -bamout bams that underly the read data visualizations which appear at the bottom of ExAC browser variant pages.

exac_2015

Companion repo for ExAC paper, 2015

exac_browser

Archive of ExAC browser

exon_skipping

Collection of manually-curated variants that cause exon skipping

gene_lists

List of gene lists for genomic analyses.

gnomad-docs

gnomad_browser

gnomAD browser pre-ASHG 2018

gnomad_lrrk2

gnomad_mnv

Multi-nucleotide variants (MNVs) in gnomAD 2.1

hail

Scalable genetic data analysis.

igv_utils

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

leiden_sc

Repository to practice code review and best development practices with Software Carpentry.

matchbox

matchbox server for the Matchmaker Exchange

myoseq_reports

Creates research-only pdf reports for MyoSeq group

obo_parser

Parses ontologies in .obo format (such as the Human Phenotype Ontology) and converts them to a .tsv table.

omim

Repo for downloading and storing OMIM data

ribosome_occupancy

spidex

VEP plugin which annotates variants with Spidex scores (see http://www.deepgenomics.com/spidex/)

ssdist

VEP plugin which annotates variants with distance to nearest splice sites

tx_annotation

Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation"