Hi, it all depends on what you are doing exactly - SNV discovery, indels, structural variants - somatic or germline variants etc... A great place to start is with GATK. There is a lot of very detailed material on where to start genome analysis for many applications. gatk.broadinstitute.org/hc/en-us Its very detailed so take your time reading the relevant parts. I would start with the Best Practices.

Rana, deeply sorry to hear of your symptoms. If they aligned your DNA to a reference genome, they most likely did this as an attempt to identify a genetic mutation in a gene that is commonly seen in cancers. If they found one, it may help your doctors to identify a treatment plan by using a drug to target that mutation. CD markers help to distinguish different types of blood cells in circulation and are usually measured by immunoassays, which can indicate aberrant levels of certain types of blood cells (e.g. too many white blood cells in circulation, as in lymphoma). I am not an expert in interpreting results, only sharing what I know to hopefully help you understand the diagnostics that are being run. Wishing you a return to good health.

Can you help me understand what this is all about? First infection of what? Why do we need gnomes