📋 Requirements

R 4.2.0

🛠️ Installation

devtools::install_github("clbenoit/GermlineVarDB")

⚙️ Configuration

Save locally and edit the config file

• [Optional] browser_server_path : In the case of a local JBrowseR installation, not intended for production use
• [Optional] browser_client_url: Url to your JBrowseR server, files should be accessible from the WebBrowser used to access the Shiny app
• cache_directory : directory to store GermlineVarDB cache files in. Necessary for good app performances. If NULL, a temporary directory will be used and cache will be lost on computer restart

🚀 Run the application

GermlineVarDB::run_app(prefix = "yourdatabasename", db_path = "path_to_your_database_location", config = "path_to_your_config_file")

For example

GermlineVarDB::run_app(prefix = "lung_variations", db_path = "/home/my_databases/", config = "/home/configs/mycurrentconfir.yml")

Will launch GermlineVarDB on the following SQLite database : /home/my_databases/lung_variations.db

Demo app

💻 Run demo locally

• GermlineVarDB::run_demo_app(browser = TRUE) Will download genome reference file on first call before to start the app

• GermlineVarDB::run_demo_app() Skip references download and disable genome browser on demo app

🌐 Live demo App

See live demo

🧬 Manage your genomic variations database

The GermlineVarDB package comes with a tools suite to manage your database. Here are the more common R functions :

• GermlineVarDB::buildDB_seqone(prefix = prefix, db_path = db_path, vcf_name = "pathtovcf") Will import genomic variations found on the specified vcf (seqone format) to the selected database. More information abouth the vcf specifications

• GermlineVarDB::addMDtodb(db_path = db_path, prefix = prefix, API_key = "MD_API_key", workers = 2) Will annotate variants in the selected database. A Mobidetails account is required

• GermlineVarDB::addSampleAttributes(db_path = db_path, prefix = prefix, matches_file = system.file("extdata","testdata/samples_run_match.tsv", package = "GermlineVarDB")) Add samples attributes to the selected databases. These attributes should be defined in a tsv file

• GermlineVarDB::compute_frequency(db_path = db_path, prefix = prefix ,attribute = "run") Compute genomic variant frequencies accoding to a specific samples attribute. Previous Example : According to sample sequencing run belonging.

• GermlineVarDB::CNVtodb_seqone(db_path = db_path, prefix = prefix, cnvfile_path = system.file("extdata","testdata/cnv.tsv", package = "GermlineVarDB")) Will import copy number variations found on the specified cnv file (seqone format) to the selected database.

• GermlineVarDB::QCtodb_seqone(db_path = db_path, prefix = prefix, qcfile_path = system.file("extdata","testdata/QCs.csv", package = "GermlineVarDB")) Will import copy number variations found on the specified QCs file to the selected database.

🔜 Incoming features

• Feed database with vcf produced by sarek nf core pipeline
• Possibility for the user to save filters and parameters presets and choose a default one
• Add in silico panel lists usable as filtering option
• Possibility for the user to upload a list of preferential transcripts, default use the canonical one in sample variants table -> cleaner view

⚠️ Troubleshouting