Whoops; fixed!
> This can be quite difficult to figure out if an A>C at a particular position is meaningful or not.
What about https://promethease.com ?
Whoops; fixed!
> This can be quite difficult to figure out if an A>C at a particular position is meaningful or not.
What about https://promethease.com ?
Note: I do this work for cancer genomes (WGS, tumor and germline). Promethease is not something that I use for annotations, but my workflows are significantly more complex.
The biggest thing I’d look out for is mindset. Biology is very different from comp sci. CS is very deterministic. You change something here, you get a result there. Biology, on the other hand, is very messy. There are compensation mechanisms on top of compensation mechanisms, and everything favors life. If you see a deleterious variant, that still doesn’t mean you’ll see a phenotype (effect on you). It’s quite a different world and can be very scary if you are looking at your own data.
And to complicate things further, one variant in a gene could do nothing if the other copy is still good. Even if you have two bad variants in a single gene, they might be on the same allele (from the same parent). In which case, you still have one good copy! It’s like how Iceman got hit twice in the same engine at the end of the original Top Gun. He still had one good engine to get home. For many genes, that’s all you need. For others, you might not even need one good copy as other genes could take over the same job.
Yes, there are some variants that you don’t want to see. Things that might indicate high likelihood of disease down the road. But even that is bound by statistical probabilities. Good news — some of those can’t be seen by this type of sequencing.
You’re absolutely right though — it can be scary. After looking at many genomes, it can be amazing that we all work as well as we do.