detection of single nucleotide variations with RNA-seq

Question

[mlemusfuentes]

hello everyone,

I need know if someone has performance detection of single nucleotide variants (SNVs) using RNA-seq data. I know that the gold standard method is whole genome or exome sequencing (WGS or WES), but I need to implement a method less expensive for the determination of SNVs. I found a scientific paper written by Chepelev et al. 2009 which is entitled "Detection of single nucleotide variations in expressed exons of the human genome (https://pubmed.ncbi.nlm.nih.gov/19528076/). You know it protocol?, what are your appreciations of detection of SNVs using RNA-seq data?, what would be the weak points of this type of analysis?

I will appreciate any comments or advice

Answer 1

[ATpoint]

This has been discussed many times before, please check previous threads:

Rna-Seq Data Variant Calling

Inferring genotype based on RNA sequences (RNA-seq variant calling)

What is the advantage of variant calling using RNA-seq technique?

RNA and DNA variant difference

and others via the search function.

I think the take-home message is that you can try and feed your RNA-seq data into a variant caller but you would need to more extensively confirm interesting variants with independent experiments. You are obviously limited to expressed exons.

[Kevin Blighe]

Moved to answer