I am really new to the field of genome analysis (I've got a computer science background). At the moment I am dealing with the topic of variant calling and decided to use / understand the HaplotypeCaller. So please apologize my stupid question.. I do not understand why the HaplotypeCaller does the whole alignment step again (or did I understand that wrong?). What is the purpose to use the BAM file and re-align it?
Best regards, Kristina