The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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?