Genetic variation calling (SNPs) from bulk RNA-seq dataset

Question

[Shicheng Guo]

Dear All,

Is there anything should be careful for the workflow developed for Genetic variation calling (SNPs) from bulk RNA-seq dataset. Is there mature established workflow for SNP identification from RNA-seq data?

Thanks.

Answer 1

[Istvan Albert]

I believe that DNA based variant callers suffice, for a review see the following paper:

RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species, Frontiers of Genetics, 2021

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273700/