ConsDB 1.0 Tool for creating consensus genomes from variant databases.

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.