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.
Thank-you,
Jessie