finding mutation from RNA seq data

Question

[Learner]

Hello,

I have many samples, I am searching to find whatever package or software which is used for finding mutation using the RNAseq data.

I already know about InVex and mutSig . is there any other software or package available?

Answer 1

[Ram]

You can find this paper helpful describing SNPiR pipeline : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676881/

[Ram]

For a moment there, I was wondering "When did I modify this question?"

Answer 2

[WouterDeCoster]

Have a look at the GATK best practices for calling variants in RNA seq data

Answer 3

[Medhat]

here there is a list of tools

https://omictools.com/variant-detection2-category

from those I suggest GATK or samtools

a nice review to compare different tools
Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations