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Indel realignment for MuTect2 in GATK 4.0
Hello I have already read that the indel realignment is deprecated in GATK 4.0, as HaplotypeCaller does the realignment, but what about MuTect2?
In one of your posts ( https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2 ) I see you already have data where indel realignment was done. Was this intentional?
How do I proceed with the pipeline then?
Should I run indel realignment on my data with 3.8 and then use 4.0 Mutect2?