VAF by Read Count and VAF by Cell Count are two different methods to calculate the average variant allele frequency of a particular variant.
VAF by Read Count considers sequencing reads across all genotyped cells, disregards cell-barcode identity, and computes the fraction of mutant sequencing reads. Conceptually, this method is comparable to conventional bulk sequencing (top panel in the picture below).
VAF by Cell Count considers genotypes (alleles) across all genotyped cells, disregards cell-barcode identity, and computes the fraction of mutant alleles (bottom panel in the picture below).
Both, VAF by Read Count and VAF by Cell Count are expected to be comparable and do not deviate more than 1.5-fold.
If VAF by Read Count > VAF by Cell Count by more than 1.5-fold, it may be indicative of copy number alterations (e.g., mutant allele amplified).
If VAF by Cell Count > VAF by Read Count by more than 1.5-fold, it may be indicative of an artifact. Considering the variant for downstream analysis is not recommended.