Hello, I am trying to find one or more unknown pathogenic variants in a human genome. They may be extremely rare, or novel. It does not closely resemble any disease presentations that I can find. I bought a Promethease report, and it's not listed, so I guess that means it's not a known exome SNP variant.
I don't have much energy for brain function, so everything is very difficult for me. (I don't know why though, that's the big question.) I would like some suggestions about which tools I should use, in what order, to find an unusual variant or combination of variants. I don't know what kind it is. I tried to start with annotating and FilterFuncotations, but it returns an error, which already has a separate thread. I don't know exactly what to expect from FilterFuncotations, but if it only uses a database of known SNPs, then I don't think it will be of much use, even after I get it to work. So, what should I look for?
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