SNP discovery & genotyping in humans vs. flies

Question

[kgbenn123]

I am led to believe that there are significant differences in how we discover and genotype SNPs from flies and humans, however I'm not sure why. I was told that the ability to create inbred lines of model organisms allows us to do a simpler version of SNP discovery than a population of humans. Can anyone explain what the difference would be in how we approach discovering SNPs in humans vs flies?

Answer 1

[Emily]

I would guess that this is related to the fact that inbred lines will be mostly homozygous for all variants, which makes variant calling a bit easier – either it's one thing or another thing and anything in low frequency is probably just dodgy sequencing. In outbred species, such as human, there's a lot of heterozygosity which means your variant caller would need to distinguish between all one thing, all another thing or ~50:50, with the added complexity of dodgy sequencing.