A tool to import and map SnpEff annotated VCF files to COMBAT-TB NeoDB Graph database.
Prerequisites:
docker
anddocker-compose
๐ณ
Clone repository:
$ git clone https://github.com/SANBI-SA/vcf2neo.git
...
$ cd vcf2neo
Build COMBAT-TB NeoDB:
$ docker-compose up --build -d
...
Install and run vcf2neo
:
- Using
pip
$ pip install -i https://test.pypi.org/simple/ vcf2neo
...
- or via
setup
invirtualenv
$ virtualenv envname
...
$ source envname/bin/activate
$ pip install -r requirements.txt
$ python setup.py install
Import and map SnpEff annotated VCF files to genes and drugs in NeoDB:
You change the default database location (localhost
) by setting the
DATABASE_URL
environment variable to remote
.
$ vcf2neo load_vcf --help
Usage: vcf2neo load_vcf [OPTIONS] VCF_DIR
Load SnpEff annotated VCF files to genes and drugs in NeoDb.
Options:
--owner TEXT Specify owner. [default: $USER; required]
-p, --phenotype [XDR|MDR|SUSCEPTIBLE|UNKNOWN]
Specify phenotype. [required]
-a, --antibiotic TEXT Specify antibiotic. E.g. Rifampicin
[required]
--help Show this message and exit.
$ vcf2neo load_vcf -p UNKNOWN -a UNKNOWN PATH/TO/VCF_DIR
...
Exploring variant data:
Point your browser to localhost:7474 to access the Neo4j browser.
To view the schema, run:
call db.schema.visualization
Sample Cypher query:
MATCH(g:Gene)--(v:Variant)--(cs:CallSet)
RETURN g.name as gene, v.consequence as variant, cs.name as file
LIMIT 25