GATK4 -known-sites input Recalibrate Base Quality Scores

Question

[missTique]

I am working with a non-reference plant species that I want to call variants from after aligning to a closely related species reference genome. I am following the GATK4 best practices pipeline, but I would like to know how I should proceed with the BaseRecalibrator step, given that it requires "-known-sites" input.Since the data I am working with is non-reference, I don't have any known sites. What could I use as an input for this step? Or am I forced to move on without it?

[K.patel5]

There is some guidance on this on the official site. https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-BQSR-

Essentially you will have to create your own database of variants, and then use this as your --known-sites.