The integration of omics has enormous potential that can be exploited for variant discovery. Several algorithms have been developed to detect somatic variants in an integrated fashion but, to our knowledge, there is still no strategy for germline variant calling. On this basis, we have developed a strategy to identify germline variants by integrating both WES and RNA-seq data. This integrated strategy identifies short variants (SNPs and indels) from raw sequence data, which are classified into six groups to improve variant interpretation: strong-evidence, DNA-only, RNA-only, allele-specific expression (ASE), RNA-editing and RNA-rescue variants. Four samples were analyzed and we show an increase in the number of identified variants without a great effect on performance compared to the exclusive use of WES data, allowing the validation of the variants identified by both types of data (strong-evidence variants), and the identification of RNA-editing and ASE. This integrated strategy provides a method to identify germline SNPs and indels from WES and RNA-seq data taking full advantage of both omics to broaden the range of identified variants and perform variant validation.