Suggestions to find pathogenic variant
Answered
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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Hi Joyce Anon,
I provided an alternate explanation to find a pathogenic variant in my comment here: https://gatk.broadinstitute.org/hc/en-us/community/posts/5573282748699/comments/6091451917083. Did this answer your question?
Best,
Genevieve
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No. I was hoping for help with finding novel variants that might help explain some health issues, so that treatments can be found, and the cognitive dysfunction can be improved. But I don't have enough cognitive function yet, to find out what to do. That error was simply the forced stopping point that I reached, after spending a week or so learning this software and linux. But I need help finding novel variants. I have identified a lot about the nature of the problem, but still haven't pinned down enough genetic problems to explain it.
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Hi Joyce Anon,
I would recommend checking out the book Genomics in the Cloud. It's a really great resource for starting out in this field and will walk you through the steps you are looking to do.
One of our users (KT Pickard) wrote a blog post on Terra all about his process searching for answers in his family's genes. KT also published a book club video series working through Genomics in the Cloud. Those videos are an excellent resource for learning genomics and reading the Genomics in the Cloud book.
Hope these resources can help you out!
Best,
Genevieve
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