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lower quality score after BQSR
Happy new year! I am doing BQSR in a non-model organism. So I did a first round of BQSR, and extract the highest 20%SNPs according the quality score ("QUAL"column) to use as a known dbSNP dataset. But I finally found that, the mean quality score after BQSR is lower than the initial one (both of them run with -unifiedgenotyper). I wonder if it is reasonable?