The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

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?

Best Answer


Sign In or Register to comment.