Adapting cellSNP for gene-of-interest / indels / multiple scRNA-seq samples

[ychenab]

Hi Yuanhua,

I have three suggestions/questions about cellSNP and cellsnp-lite:

1. Would you consider using the "start" and "stop" parameters in pysam.pileup to allow users to achieve faster SNP detection within a region/gene of interest?

2. One of my gene of interest is known to be frequently disrupted by frameshift mutations / indels, but cellSNP only support single-nucleotide variant detection. Could the pipeline be modified to consider indels?

3. Is it possible to input two or multiple scRNA-seq samples and identify sites that are different across samples?

Thank you!

Best regards,
Yiyun