I am working on a project identifying SNPs/SNVs of a few sequences and was wondering if there is a good work flow for conducting such an analysis with Galaxy? I have vcf and BAM files (already indexed) available for use and would ultimately like to align them to a ref sequence and see what SNPs I can find. One small caveat: these files include whole chromosomes worth of data.
While I can find SNPs manually in IGV, it is tedious, and I am sure there is a way to solve this issue using bioinformatics. Ideally I would like to use vcf files, because they include genotypes.
Any suggestions? Is it even possible?
Thorough, step-by-step answers would be appreciated (I'm a rookie, can you tell?).
Thanks for your time in advance!