Question: Is it possible to call SNPs or splicing variants from single cell gene expression data using 10x software?
Answer: 10x Genomics supported software (Cell Ranger) currently does not enable SNP or variant calling. However, there are community-developed tools for calling SNPs or variants from single cell gene expression data, listed below. These tools are not supported by 10x Genomics, so any questions or comments should be submitted through gitHub directly to the tool developers.
In addition, this website (https://www.scrna-tools.org/) contains a more comprehensive list of tools. Using the the 'Filter by category' and selecting 'Variants' you can identify several more variant calling tools (https://www.scrna-tools.org/tools?sort=name&cats=Variants ), including the few listed above. Please be aware that some splicing analysis tools may require sequencing 10x data with long read sequencing technology (for example: https://github.com/LuyiTian/FLAMES).
Disclaimer: This article is provided for instructional purposes only. 10x Genomics does not support or guarantee the listed tools or code.