Bash Script for a specific SNP

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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!


SARS-CoV-2


BASH


SNPS

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