Question: Is it possible to do single cell genotyping at a specific locus?
Answer: At this time the standard Cell Ranger pipeline does not do single cell genotyping at a specific locus. There is a tool available called VarTrix which may be of interest to you -- however please note it is not supported by 10x Genomics, so any questions or comments should be submitted through gitHub:
"VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data. VarTrix will take a set of previously defined variant calls and use that to identify those variants in the single cell data. VarTrix does not perform variant calling. VarTrix is useful for evaluating heterogeneity within a sample, which means that the types of variants that will be useful are either somatic or contained within a copy number variant (CNV) event."