Let's say you're searching through a VCF with germline variants. You find a variant that's present in only one person. In addition, this person is homozygous for that variant. The chances of finding a variant like this by random chance are pretty small. Only a handful of variants should be like this. Instead, you find over a thousand. Some are close to each other on the same person.
Also, the average person in a study population tends to only have a few hundred or thousand unique variants - about the same as the number of single homozygotes.
How likely is it that this variant call is the result of an early somatic SDSA repair vs. something else?
How can I find out if these "unique" spots are double-stranded-break/recombination hotspots?
I'm just looking for opinions. Any input is welcome.
Probably the best publication on variants I've read so far. They do an amazing work on singletons, just like your situation.
http://www.nature.com/nature/journal/v536/n7616/full/nature19057.html
Thank you for the response. I couldn't find a comparable situation however.
My first idea would be that that person is from an entirely different population than the rest of the individuals you are working on.
This may be possible, but these sorts of variants occur within 1000 genomes subpopulations as well. But thank you for the response. It may be a good idea to find out who these variants are coming from.