SARS-CoV-2 Consensus caller

SARSConsensusCaller is a wrapper python script for fast consensus sequence calls based on generated vcf files

HOWTO

Installation

1. git clone https://github.com/bioinf-mcb/SARSConsensusCaller.git
2. cd SARSConsensusCaller
3. conda env create -f consensus_caller.yaml
4. conda activate consensus_caller

Running

1. cd [...]/SARSConsensusCaller
2. python call_consensus.py -f <vcf_folder> -r <reference_fasta_path> -o <output_folder>

Output

Output will be placed within specified output folder within VCF directory