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Base quality score recalibration makes all reads low quality?
I am running the GATK pipeline on barley exome capture data. In order to verify that we are doing a good job with realigning around indels and are calling true variants, we are comparing our alignments to known variants from Sanger resequencing. We are using the latest version of consed (26) to view our BAM files. However, we noticed that after base score quality recalibration, almost every base seems to be marked as Phred20. Before recalibration, our scores were Phred30 and above, and our alignments looked relatively clean.
Is there an option in the base quality recalibrator tool that would affect this? How can we avoid tamping down our quality scores so aggressively? Thank you.