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Created 2015-12-10 16:33:06 | Updated | Tags: haplotypecaller alignment swa
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Hello community,

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