GitHub Overview#
This section gives an overview of the GitHub repositories relevant to the VarFish project.
All are in varfish-org, version 2.0 of the Apache license is used.
Direct Importance#
The following repositories are directly important and provide functionality used by the system.
name |
license |
synopsis |
|---|---|---|
annonars |
MIT |
precomputed variant, region, and gene annotation |
annonars-data-clinvar |
MIT |
ClinVar data builds for annonars |
cada-prio |
MIT |
phenotype-based prioritization based on knowledge graph embeddings |
cadd-rest-api |
MIT |
REST API wrapper for CADD-scripts |
cadd-rest-api-mock |
MIT |
mocking the CADD REST API server for VarFish development |
clinvar-data-jsonl |
MIT |
weekly ClinVar releases as JSONL plus useful aggregation |
clinvar-this |
MIT |
ClinVar submission and XML dump file parsing |
mehari |
MIT |
transcript effect annotation and tx model information |
mehari-data-tx |
MIT |
transcript data builds for mehari |
varfish-db-downloader |
MIT |
Snakemake workflow to download public data |
varfish-cli |
MIT |
command line interface for VarFish REST API |
varfish-dev-docs |
MIT |
documentation for developers |
varfish-docker-compose-ng |
MIT |
setup VarFish with Docker Compose |
varfish-server |
MIT |
VarFish web server |
varfish-server-worker |
MIT |
heavy lifting in varfish-server written in Rust |
viguno |
Apache |
HPO ontology access and full-text search |
Indirect Importance#
The following are dependencies of the one in Direct Importance maintained by us and housekeeping tools.
name |
license |
synopsis |
|---|---|---|
biocommons-bioutils-rs |
Apache |
(partial) port of biocommons/bioutils to Rust |
hgvs-rs |
Apache |
port of biocommons/hgvs to the Rust programming language |
rocksdb-utils-lookup |
Apache |
utility library for using RocksDB as lookup tables |
seqrepo-rs |
Apache |
a port of biocommons/seqrepo to the Rust programming language |
Experimental#
The following contain experimental, under development, or unfinished code.
name |
license |
synopsis |
|---|---|---|
scarus |
Apache |
automated evaluation of ACMG rules |
varfish-clinical-beacon-client |
MIT |
client for clinical beacons API proof of concept |
varfish-wf-validation |
MIT |
Snakemake workflow for automated validation |
varfish-cli-ng |
MIT |
VarFish CLI based on aws-smithy |
Legacy#
The following are legacy repositories.
name |
license |
synopsis |
|---|---|---|
varfish-course-scripts |
MIT |
scripts for generating the data used in the VarFish course |
varfish-wf-queries |
MIT |
VarFish (Snakemake) Client Workflow for Querying Snakemake |
varfish-docker-compose |
MIT |
legacy setup VarFish as using Docker Compose |
varfish-anno |
MIT |
convert annotation database files to Var:fish: import format |
varfish-installer |
MIT |
use varfish-docker-compose instead |
varfish-annotator |
MIT |
annotate variants for import into VarFish server |
varfish-data-igsr |
MIT |
repository for building IGSR data sets for use in VarFish |