Hi all, I'm working on a variant calling pipeline based on the following link:
Now, in the "Improvement" section, which mainly uses GATK, it says that I should realign the bam file and then recalibrate and mark the duplicates. What is unclear to me is which bam file is used as input for each step. For example, is the realigned bam file the input of the recalibration step?
I should note that I'm using a single bam file, 1 library.
Thank you, Alon