Hi, I have some single cell genome sequencing data and I'd like to know if there is any good solution for CNV detection. I hear that CNVkit is a good choice to detect CNV for bulk data, but I don't google any thing about single cell.
CNVkit should work fine for single cell sequencing data. It doesn't do anything specific to use the single-cell assumption initially, but you can use the
cnvkit.pyp call -m clonal command to enforce the assumption that the cells are all identical, with a given ploidy if it's known, otherwise assuming diploid. This is similar to the "quantization" step described by Baslan et al. (above/below).
It's definitely worthwhile to see what else has been developed specifically for single cell data. CNVkit integrates relatively easily with other tools, especially if you are willing to do a little bit of scripting or command-line processing.
You can take a look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069701/
They use a custom approach to CNV calling from single cell data but they provide a good guide and access to code as supplemetary material. Not a full blown package, but it might be helpful.