Hello GATK Team,
I wonder if IndelRealigner work the same way as the indel realignment included in HaplotypeCaller. Do they use the same algorithm? Does this mean that I don't need to realign indel for my bam using IndelRealigner if I use HaplotypeCaller later on?
If I use both IndelRealigner and HaplotypeCaller in my pipeline, will that affect the output from HaplotypeCaller?
Thank you very much!
Felicia