Excluding/keeping reads from normal cells in the bam for BAFExtract

[kzb193]

Hello Dr. Akdes,

I would like to use CaSpER to a 10x scRNA-seq tumor dataset, and I know the group of normal cells. The bam file contains reads from all the cells ( it has both the normal and the cancer cells). Do I need to filter out the reads from the normal cells from the bam file before using BAFExtract? Can you please suggest the best practice in this case for identifying regions with copy number variation using CaSpER?