We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
BQSR and False Negatives?
I am looking at GATK Best Practices for Data Processing and Germline Variant calling. I see that the workflow calls for base quality score recalibration using BaseRecalibrator [https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_bqsr_BaseRecalibrator.php] which assumes that any base that is a mismatch to the reference and not in the variable site DB are sequencing errors (aka low quality). It seems that if a true variant is rare in the population, and not in the variable loci DB, then it would get an artficially low recalibrated quality score.
In your all's experience, has this lead to false negatives when you ave tested the workflow on positive control samples? If not, can you help me reason why it would not lead to missing the true positives that are not masked during the model calibration phase?