run SComatic with not FACS-sorted data

[giorgiagandolfi]

Hi, I am working on 10X scRNA data of AML patients. The samples were not FACS-sorted, for this reason barcodes were labelled in three different classes: microenvironment, malignant and control. I also have the cell types assignment for each barcode, independently from the class. Since I am interested in finding somatic mutations specific for AML, I would like to know if it is better to filter the input possorted_genome_bam.bam with only malignant barcodes or by keeping it as it is.

In the second option, can be possible to use as "cell type assignment" the class labelling instead of the biological cell type?
Thanks in advance
Giorgia