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.
Pre-adapter artifacts (in hybrid selection)
Various sources of error affect the hybrid selection (HS) process. Pre-adapter artifacts are those that arise in the preparation step(s) prior to the ligation of the PCR adapters. These artifacts occur on the original template strand, before the addition of adapters, so they correlate with read number orientation in a specific way.
A classic example is the shearing of target genomic DNA leading to oxidation of an amine of guanine at position 8 8-oxoguanine (8-OxoG, OxoG) (doi:10.1093/nar/gks1443) (see also OxoG entry in this dictionary).