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.