loqusdb

Small tool to set up a local variant database. If you find Loqusdb useful in your work, please cite the article.

Right now Locusdb uses mongodb as backend for storing variants, but there should not be a huge difference to use another database manager.

Find more detailed instructions and examples in the documentation.

Installation

poetry install

or

$git clone https://github.com/moonso/loqusdb $cd loqusdb $poetry install

Idea

Tool to keep track of what variants that have been seen and in what families they have been observed. This is NOT a tool to create a true frequency database. It will basically count the number of times we have seen a variant in any individual. We will also keep track of the variants that have been seen in a homozygous or hemizygous state.

Variants are stored by providing a VCF file and a (ped or ped like) family file.

Loqusdb will first check if the VCF file adheres to the VCF format.

The tool will then check all variants if they have been observed in any of the individuals in the family.

When the variants are added:

• Either the variant exists, in this case we increase the number of observations with one
• Or this variant has not been seen before, then the variant is added to the database

Command Line Interface

``` $ loqusdb Usage: loqusdb [OPTIONS] COMMAND [ARGS]...

loqusdb: manage a local variant count database.

Options: -db, --database TEXT Defaults to 'loqusdb' if not specified -u, --username TEXT -p, --password TEXT -a, --authdb TEXT If authentication should be done against another database than --database

-port, --port INTEGER Specify the port where to look for the mongo database. [default: 27017]

-h, --host TEXT Specify the host where to look for the mongo database. [default: localhost]

--uri TEXT Specify a mongodb uri -c, --config FILENAME Use a config with db information -t, --test Used for testing. This will use a mongomock database.

-g, --genome-build [GRCh37|GRCh38] Specify what genome build to use -v, --verbose --version Show the version and exit. --help Show this message and exit.

Commands: annotate Annotate a VCF with observations cases Display cases in database delete Delete the variants of a family dump Dump the database export Export variants to VCF format identity Search identity collection index Add indexes to database load Load the variants of a family migrate Migrate an old loqusdb instance profile Loads variants to be used in profiling restore Restore database from dump update Update an existing case with a new type of variants variants Display variants in database wipe Wipe a loqusdb instance ```

Database

Connecting

Connection can be specified on command line with --database, --username, --password, --port, --host and/or --uri. Or these options can be sent with a config file that can take the same options:

yaml uri: mongodb://loqusdb-username:loqusdb-pwd@localhost:27030/loqusdb-rd?authSource=admin db_name: loqusdb_test or yaml host: localhost port: 27030 username: loqusdb-username password: loqusdb-pwd authdb: admin db_name: loqusdb_test

Mongo

The collections are defined as follows:

Case

python { 'case_id': 'case_id', 'vcf_path': 'path_to_vcf' }

Variant

python { '_id': 'variant_id', 'chrom': 'CHROM', 'start': postition, 'end': end postition, 'ref': reference base(s), 'alt': alternative base(s), 'homozygote': number_of_homozygotes, 'hemizygote': number_of_hemizygotes, 'observations': number_of_observations, 'families': ['family_id', ...] }