Question: variant calling using reference transcriptome
1
gravatar for prasundutta87
2.9 years ago by
prasundutta87360
prasundutta87360 wrote:

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)

ADD COMMENTlink modified 8 months ago by eric.audemard10 • written 2.9 years ago by prasundutta87360
0
gravatar for Kevin Blighe
13 months ago by
Kevin Blighe53k
Kevin Blighe53k wrote:

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

ADD COMMENTlink written 13 months ago by Kevin Blighe53k
0
gravatar for eric.audemard
8 months ago by
eric.audemard10 wrote:

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.

ADD COMMENTlink modified 8 months ago • written 8 months ago by eric.audemard10
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