Next generation sequencing (NGS) technologies are now widely used in medical research. NGS provides an unprecedented opportunity for high throughput analysis of genetic variations warranting their use in molecular diagnostics. However, among other obstacles, their adoption in clinics poses challenges in the provision for accurate and timely data analysis. A bioinformatics workflow for the analysis of the large amount of data from raw reads to final annotated variants suggesting their functional consequences with clinically actionable or reportable sensitivities and specificities is important. We have developed a number of targeted panels using NGS for the diagnosis of a number of haematological abnormalities and cancer