SComatic with a single cell type but with germline reference

[northerngasc]

Hi,

Thanks a lot for the excellent tool!
We have single-cell data from sorted myeloma cells in which we would like to detect somatic variants.
Since they are sorted we do not have (or very few) other cell types from the same samples.
However we have (1) single-cell data from normal plasmocytes from healthy donors and (2) WGS from normal and tumor from the same patients.

We were planning to:

• merge a tumor bam file with healthy plasmocytes to run SComatic with 2 cell types "myeloma_cells" and "healthy_plasmocytes". The healthy cells are not from the same patient but would carry the same "technical artifacts"
• use the vcf of germline variants identifies in WGS data from the same patient to accurately remove germline variants.

Would it make sense in your opinion?
Thanks a lot,
Eric