📋 Requirements

R 4.2.0

🛠️ Installation

devtools::install_github("clbenoit/GermlineVarDBTools")

🧬 Manage your genomic variations database

• GermlineVarDBTools::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

• GermlineVarDBTools::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

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

• GermlineVarDBTools::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.

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

• GermlineVarDBTools::QCtodb_seqone(db_path = db_path, prefix = prefix, qcfile_path = system.file("extdata","testdata/QCs.csv", package = "GermlineVarDBTools")) 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

⚠️ Troubleshouting