I would like individual level genotypes for a SNP that appears in the 1000 genomes browser and dbSNP. When I pull the VCF for the region using the Data Slicer, I get calls for SNPs around my Mystery SNP but not for my actual mystery SNP. Pulling down the VCF and searching with tabix gives the same result. It's not clear to me why this SNP doesn't have individual calls. Is the most reasonable way to go forward to pull down the region around the SNP from the source BAM files and call genotypes with mpileup? If so, is there a better way to do this than manually scripting it out? Thanks.
My suggestion is to check the individual call set first, which are available here. If you cannot find the SNP in all of them, it is likely to be a false one. A caveat is most of these call sets do not provide accurate genotypes. When you can get genotype likelihoods in GL or PL, you can use beagle to impute genotypes.
Another possibility is that this SNP was called in the early phases of the 1000G, but removed in later phases as calling methods improved. Some of those old SNPs might be in older versions of dbSNP, which could cause confusion.