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I used the haplotype caller to make consensus sequences. I also tried to make consensus sequences using samtools. What I noticed that samtools put in some places 'N' but the GATK consensus doesn't put N instead it is the same base what reference sequence has. When I checked in using Tablet, I found that samtools consensus sequences were correct. Can you please explain how the consensus sequences are made in gatk when there is no read support for a position. Is it simply assume the reference sequence bases as that position to be correct and put that as a consensus sequence?