variant calling using reference transcriptome

Question

[prasundutta87]

Hi,

Is there any tool which uses a reference transcriptome to call variants instead of a reference genome ? I will also like to use the reference transcriptome for variant annotation as well and would like to know if any variant annotation tools allows that. I did not find any tool optimised to work with a reference transcriptome for the above two jobs. Any help or suggestions are welcome.

(P.S. I have RNAseq reads to call variants from)

Answer 1

[Kevin Blighe]

I don't believe any of us should be encouraging variant calling from RNA-seq. Here is why:

A: Inferring genotype based on RNA sequnces

Answer 2

[eric.audemard]

If you are interested by calling any type of variants in a targeted region of the transcriptome (not in the whole transcriptome), maybe km could be useful for you.

We are actually in peer review process, but a pre-print version is available on bioRxiv and feedback is always appreciate.