GATK AnalyzeCovariates No improvement/Sequencing Bias Removal
I used the GATK bootstrap method to re-score my quality scores/eliminate systematic biases for my population genetic dataset in a non-model organism. However my "after" score doesn't improve at all from the before. The GATK best practices suggest running until you converge; my data have converged, without the loss of the systematic biases. I am if it is possible to get rid of these biases, and if not, what advice people may have moving forward in my variant call pipeline.
My plots from running AnalyzeCovariates showing the persistent biases both before and after base re-calibration: Any help or insights would be very much appreciated.
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timothy.delory •
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https://ibb.co/8DD6PYP here is the URL to the image of the Analyze Covariates plots.
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