Fig. 1

Overview of OncoGEMINI database creation and usage. a Genetic variants from a VCF file are first annotated by the user with either SnpEff or VEP and then additional user-determined annotations can be added to the SnpEff or VEP annotated VCF file using the vcfanno tool. b The fully annotated VCF, along with a sample manifest file, is then used to create an OncoGEMINI database via vcf2db. Once the OncoGEMINI database is created, users are able to c create their own customized queries with the query command or d select from built-in tools (such as bottleneck, loh, or truncal) to filter variants. To better select and focus on specific variants, users may combine tools and queries with included annotations to further filter the number of variants