Online databases version control
For each session of annotation, WGAViewer will automatically check the latest genome build, HapMap release, etc and align the database loaded with the latest genome build. The version of the databases used will be displayed in the upper right table in Genic Annotation (Gene context panel). No manual setup is necessary.
GAViewer uses a “Dynamic Genome Build Anchoring” algorithm to control for the genome coordinate discrepancies during the version updates. Instead of directly using genome coordinates from diverse sources, we have treated the genetic markers as anchors and always used a fast hashtable-matching to map these anchors into the uniform Ensembl build version. This uniform build version, together with the version from other sources, is stored in the annotated project file and can be referred to in the later interpretation. This dynamic procedure helps to interpret the WGA results using the most updated transcripts and SNP coordinates, and avoids discrepancy between different major builds used in different sources (for example, build 36 and build 35), or even between different subversions (for example, build 36: Ensembl version 46.36h and 43.36e). This procedure is implemented in all the annotation routines, most importantly, in the gene and SNP searching functions. We noticed that sometimes these discrepancies could be up to ~200kb, which could potentially lead to very different gene/SNP contexts and hence result in different interpretations and hypotheses.