I am a trainee working with GATK. In the clinical lab where I am working, we use GATK3 and I am learning creating my own pipeline.
In the in-house pipeline we perform local realignment around indels by the tool RealignerTargetCreator and IndelRealigner. However, following the GATK4 best practices this step is not mentioned, why?
After marking duplications, GATK4 jumps to Base (Quality Score) Recalibration while in the in-house pipeline we mark duplication, local realignment around indels and then recalibrate.
GATK4 link https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery
There was a previous discussion regarding this: Realignment disappeared in gatk4