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HaplotypeCaller Re-Alignment Step
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?