Dear people, I am a medical doctor and had an exceedingly interesting interaction with a geneticist of a large paediatric hospital who gives genetic counselling for kids with autism / epilepsy / nervous system malformations.
He told me about all of the data management hurdles he has to overcome from when he receives an NGS VCF file (from panels to exome, mostly germinal cells) to when he can issue a report identifying clinically significant variations.
The process overall takes several months and I'd like to help him to shorten the overall workflow.
Can anyone advise tutorials,documents, todos that can give ideas on how to help these people ?
Can anyone help me to identify the main logical steps involved in this process ?
From what I understood they use an annotator called ANNOVAR and then spend quite a lot of time on an excel file generated by this tool.
Thanks for any help.