Most SNP caller, such as HaplotypeCaller apply bayes method to call SNP. HaplotypeCaller use 1KG / dbsnp data set as prior probability.
This got me thinking what prior does 1KG use. It turns out that 1KG set 0.001/base as prior. This seems reasonable given that the data before 1KG shows the average SNP occurrence is 0.001.
Then the question remains. What did projects before 1KG use as prior? Or those early project did not use bayes? Then what methods did they use?