Bash Script for a specific SNP

Question

[Sam]

Beginner here. Trying to look for a specific allele presence/absence in a group of fasta files for SARS-CoV-2 genomes. Also not sure if I should use the first/original sequence out of Wuhan as the reference genome or the first genome sequenced with the allele of interest to call the SNP. I am writing this just with bash, I don't really know R or Python enough to use it. Any help, tips, tricks much appreciated!

Answer 1

[GenoMax]

Not sure what kind of data you are starting with but there are well established pipelines for this analysis. You should use one of those if you can.
SARS Cov2 NGS data analysis pipeline
COVID-19 analysis pipelines