My intention to carry out NGS is to find out somatic/genomic mutations along with Indels and Copy numbers in the normal and case DNA samples. May I know what other clinical data analysis I could carry out!
You can do what is called Genome wide association study --- GWAS. You can build Bayesian and other math models using the presence of mutations and other clinical and laboratory data. You can try to predict and classify the outcome or a disease clinical course using the modern machine learning methodologies. Look for Bioinformatics books by Springer and relevant reviews on EBSCO (commercial or free at the city library) and HighWire Press (free), DOAJ, GoogleScholar, Scielo (also free). BW.