05/06/2015 - Paper describing analysis of variation data for 40+ rat strains published in BMC Genomics

The paper Genomic landscape of rat strain and substrain variation by Hermsen et al which describes the analysis of whole genome sequencing data for 40+ rat strains is now available online.  As stated in the abstract, the authors "present a comprehensive, multi-sample and uniformly called set of genetic variants in 40 rat strains, including 19 substrains."  Existing sequences were aligned to the newer RGSC v5.0 assembly and analyzed using a single, consistent variant calling algorithm to facilitate comparisons across the strains.

The paper is now available in BMC Genomics.  SNVs and indels from this dataset have been incorporated into RGD's Variant Visualizer and the JBrowse genome browser.  Look in the data for assembly v5.0 for strain symbols where the source is "(KNAW)".  The data is also available for download from RGD's FTP site.