How do I detect copy number variation from data generated by scNuc-seq?

Question

[wp.hou3]

I have some cells sequenced by scNuc-seq technique including .fastq, .bam files and processed gene expression. I want to detect the copy number variation(CNV) for each cell, in order to differentiate glioma cells from normal cells. I've searched online and found this list consisting of 158 CNV analysis tools (https://bioinformaticshome.com/tools/cnv/cnv.html). However, these tools target at different data modalities, for example, CONICS was developed for scRNA-seq according to the manual. Does anyone know which tool can specifically be used for my data? Thanks a lot!

Answer 1

[jared.andrews07]

I don't know of any specifically for scNuc, but my guess is that CONICSmat or inferCNV are going to be your best bets.