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Updated WGS pre-processing workflow

Dear GATK,

-As per GATK 4.0.0 best practices guidelines, it is my understanding that no indel realignment step is performed anymore. Is this correct? If so, why not?

-During the pre-processing stage of a mapped BAM file, does the relative order of sorting by coordinate vs. marking (&, in my case, choosing to remove) duplicates matter? I've seen both relative orders in different scripts.


Best Answer


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