GATK AnalyzeCovariates No improvement/Sequencing Bias Removal

1

Entering edit mode

3.8 years ago

timothy.delory ▴ 20

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.

Base Recalibration Measures

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.

GATK BQSR • 1.2k views

ADD COMMENT • link 3.8 years ago by timothy.delory ▴ 20

0

Entering edit mode

https://ibb.co/8DD6PYP here is the URL to the image of the Analyze Covariates plots.

ADD REPLY • link updated 3.8 years ago by GenoMax 141k • written 3.8 years ago by timothy.delory ▴ 20

0

Entering edit mode

There appears to be something wrong with your images. Please use directions here: How to add images to a Biostars post

ADD REPLY • link 3.8 years ago by GenoMax 141k

Login before adding your answer.