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Is Indel realignment removed from GATK4?
I am seeing help of GATK4 (hellbender), and for example for the tool ReadsPipelineSpark, it says, Takes aligned reads (likely from BWA) and runs MarkDuplicates and BQSR. The final result is analysis-ready reads. In the original GATK pipeline there used to be Indel Realignment between Mark duplicates and BQSR. Is it there no more in this new version?