I have sequenced scRNA-seq data and I would like to do variant calling for one gene (KRAS) so I can annotate clusters in the downstream analysis. I have looked at past posts and there doesn't seem to be a lot of consensus on what tools to use. However, I understand that I would do something like: 1) Align reads with STAR to generate a BAM file and subsequently generate a pileup file 2) Run the FreeBayes variant caller to find SNVs
Most of the tools and workflows for variant calling tend to focus on finding SNP in the entire genome, and I would only like to look at one specific gene, KRAS.
Another question I had, is what specific read depth is appropriate for variant calling only for one gene? (as opposed to the entire transcriptome). Would there be a difference?