Is there a way in which I can catalog SNPs on Galaxy? I am attempting to use my BAM file, along with my reference genome and am having a hard time finding a tool in which it can not only identify the most frequent SNP, but also catalog them (if existent).
Please see this variant discovery pipeline for SNP summary and annotation tool options: https://galaxyproject.org/tutorials/var_dip/
Alternate methods are covered in other tutorials. Please see: https://galaxyproject.org/learn/
Thanks, Jen, Galaxy team