GATK4 -known-sites input Recalibrate Base Quality Scores
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6 months ago
missTique • 0

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?

Plant Variant NGS Calling GATK • 279 views
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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.

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