Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?