Just learning the basics of bioinformatics and bash shell scripting. Is there a correct way to search for a specific allele with one or even multiple sequencing runs? I am searching for prevalence of the C2416T allele in the SARS-CoV-2 genome as a mini project. I downloaded a bunch of sequencing runs, I think I need to convert them to bam file type than I am not sure how to call for one specific SNP, especially in a loop for 5-7 runs. Can this be done with bash?
I was looking into variant calling from a bam file type using vcf and I can't find a way to call for one specific snp on multiple bam files at once. Ideally I would want to filter the variant out of the .bcf files or use grep since I sort of understand those the most and I’m not working with a large amount of data or a human genome.