ConsDB

A Python tool for interfacing with large variant databases and performing consensus genome operations.

Written by Benjamin Kaminow

Usage

The main ConsDB script can be run as follows:

cd consdb
python ConsDB.py <run mode> [arguments]

Where <run mode> is one of the following:

• Parse - Parse database files into ConsDB files
• Filter - Filter a VCF file to remove major alleles
• Merge - Merge multiple ConsDB files
• Cons - Create a consensus VCF file
• FA - Create a consensus FASTA file

Arguments for each run mode can be viewed by passing -h as the sole argument.

Back-End

ConsDB utilizes an object oriented back-end, which can easily be incorporated into pipeline/scripts. Documentation for this back-end is found in the docs subfolder.