Variant calling in RNA-seq data is beast of a problem in and of itself. Errors due to technical factors (i.e. RT, PCR, sequencing) and biological factors (i.e. RNA editing, post-transcriptional modifications, allele specific expression) are common. RNA-seq data is noisy.

Also depending on if you are using scRNA-seq vs bulk (multiple locations or time points?) your approach may vary. For latter you need to deconvolute the variants within your samples (assuming you are comparing within an individual).

For simple manual variant calling you could check out deepSNV in R: https://bioconductor.org/packages/release/bioc/html/deepSNV.html

For building your trees you could check out SCITE which is generally used for tumor phylogenetic: https://github.com/cbg-ethz/SCITE

Another tool for transcriptome evolutionary analysis: https://academic.oup.com/gbe/article/11/11/3276/5586986

For single cell data there is also: https://www.biorxiv.org/content/10.1101/2020.02.06.938043v1

Hi there! The following tutorial Variant Calling may help you with your requirements. Please read it to see if it meets your requirements.