Systematically called variant data of public SARS-CoV-2 reads

EMBL-EBI, in collaboration with Erasmus Medical Center (EMC), Netherlands, Eötvös Loránd University (ELTE), Hungary and Technical University of Denmark, Denmark as part of the VEO (Versatile emerging infectious disease observatory) project, stream all public SARS-CoV-2 INSDC raw read data through the COVID Sequence Analysis Workflow (https://github.com/enasequence/covid-sequence-analysis-workflow) to produce a set of uniform variant calls (VCF Format). Briefly, reads are mapped to the SARS-CoV-2 reference genome, variants are called using LoFreq and annotated using SnpEff . VCFs associated with this project are unfiltered variant calls and as such may contain false positives calls and homopolymer errors. BAM files are provided as output by the analysis workflow along with a simple coverage information file. Users are advised to use these in association with the VCFs to perform any filtering tasks prior to using these VCFs for downstream analysis presentation or analysis. VEO: https://www.veo-europe.eu/