virheat 0.3

virHEAT creates a heatmap from vcf files and maps positions onto a reference genome.

virHEAT is a tool to visualize vcfs as a heatmap and map mutations to respective genes.

Ever wanted to have a condensed look at variant frequencies after mapping your raw reads to a viral/bacterial reference genome and compare multiple vcf files at the same time? Than virHEAT is for you. You can not only visualize the heatmap but also read in a gff3 file that lets you display genes harboring a mutation. This lightweight script was inspired by snipit and my variant frequency plot, getting the best visualization features of both.

SARS-CoV-2 example:

Installation

via pip (recommened):

pip install virheat

from this repo:

git clone https://github.com/jonas-fuchs/varVAMP
cd virHEAT

and then install virHEAT with:

pip install -r requirements.txt

or:

pip install .

That was already it. To check if it worked:

virheat -v

You should see the current virHEAT version.

Usage

usage: 	virheat <folder containing vcfs> <output dir> -l or -g [additional arguments]

Arguments:

positional arguments:
  input                 folder containing vcf files and output folder

optional arguments:
  -h, --help            show this help message and exit
  -l None, --genome-length None
                        length of the genome (needed if gff3 is not provided)
  -g None, --gff3-path None
                        path to gff3 (needed if length is not provided)
  -t 0, --threshold 0   display frequencies above this threshold
  --delete, --no-delete
                        delete mutations with frequencies present in all
                        samples (default: True)
  --sort, --no-sort     sort alphanumerically (default: False)
  -v, --version         show program's version number and exit

You need to either provide the length of your reference genome or if you want to get the sequence annotation you will need to provide the gff3 file.

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Important disclaimer: The code is under the GPLv3 licence. The code is WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.