vcf2db

Overview

How it works?

Output

Important notes

Create a postgres login using the following SQL statement:

 CREATE ROLE user WITH
  LOGIN
  SUPERUSER
  CREATEDB
  CREATEROLE
  INHERIT
  NOREPLICATION
  BYPASSRLS
  CONNECTION LIMIT -1
  PASSWORD 'password';

Change user to a user login and the associated password.

Requirements

Recommended system requirements:

• 8-Core CPU
• 16 GB RAM

Minimum system requirements:

• Quad-Core CPU
• 8 GB RAM

Python requirements

• Python 3.10, 3.11, 3.12 -- see http://www.python.org

Python dependencies

• psycopg2, cyvcf2

Installation

Using Conda (Recommended)

Create and activate the conda environment:

conda env create -f environment.yml
conda activate vcf2db

Running the application

To start a Database from scratch and populate with a VCF

python vcf2db.py -i your_snp_vcf_file.vcf -d vcf2db -u user -p password -l localhost -b 1000 -c

To update annotations in an existing database

python vcf2db.py -i your_snp_vcf_file.vcf -d vcf2db -u user -p password -l localhost -a

To resume an interrupted update

python vcf2db.py -i your_snp_vcf_file.vcf -d vcf2db -u user -p password -l localhost -a -r

If VEP fields changed between versions

python vcf2db.py -i your_snp_vcf_file.vcf -d vcf2db -u user -p password -l localhost -a -f

Application structure

• README.md -- This file
• LICENSE.md -- Application license model.
• MANIFEST.in -- Configures which files to include in releases.
• environment.yml -- Conda environment configuration file.
• src/ -- Source Directory
• src/vcf2db.py -- Main orchestrator and application launch file.
• src/utils/ -- utilities to write files, create sql queries, and vcf related functions.
• src/tools/ -- additional/optional tools to create a genes tables from gtf file and create synthetic gene expression data.

Additional resources

Gene table (tools/gen_genes_table.py)

Create a genes table based on gtf annotations. The genes table is made up of the gene name, gene id, gene type, chromosome, start position, end position and strand.

Example usage:

• ./gen_genes_table input.gtf --host localhost --database vcf2db --username user --password password
• ./gen_genes_table input.gtf --host localhost --database vcf2db --username user --password password --force-reload

Synthetic transcriptomics (tools/gen_synthetic_transcriptomics.py)

Generate a synthetic transcriptomics table for testing purposes.

Example usage:

• ./gen_synthetic_transcriptomics --host localhost --database vcf2db --username user --password password --protein-coding-only --seed 25
• ./gen_synthetic_transcriptomics --host localhost --database vcf2db --username user --password password --protein-coding-only --seed 25 --force-reload

To package application

python setup.py sdist

TODO