Export cell-level variant calls?

[bbimber]

Hello -

cellsnp-lite and vireo have been very useful tools to assign cells to sample. However, is there a way to export either a VCF or table that lists genotypes for every cell for the variants used? I'm interested in seeing whether particular variants are more effective in different cell types. I could do this by taking each variant, mapping to gene, and then looking at differential expression; however, using the vireo data would be more direct if that is possible.

Thanks for any help.

[bbimber]

Actually, it seems like cellsnp-lite and --genotype might accomplish this: https://cellsnp-lite.readthedocs.io/en/latest/main/manual.html#output