Variant calling on RNA-Seq data

Question

[cdjeu]

Hello Everyone,

I would like to call variants on RNA-seq data and construct a phylogenetic tree based on those variants (e.g. SNP). Could someone recommend to me the best tools to perform for instance SNP calling in RNA-Seq data? Thanks in advance!

Answer 1

[benformatics]

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

[cdjeu]

@benformatics, sorry for my late response, thank you very much for your comments and suggestions. I am going to use scRNA-sea and bulk!

[benformatics]

If you are integrating both then tools by the Beerenwinkel lab (author of a paper from above might also be of interest).

B-SCITE: https://www.nature.com/articles/s41467-019-10737-5

Answer 2

[Rongxin]

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