Annotating RNA seq Data ?

[swapnil2188]

I am trying to find out variants in RNA seq data.

I have the .bam files for the samples.

I will try and use Samtools and GATK to find out variants in RNA.

Now, as I am using Samtools I will be having .VCF files generated.

So, I was curious about can we annotate this variants using tools like annovar ?

if yes - Should I follow the same pipeline as we use to annotate DNA variants ?

if No - What are other tools or methods for annotating RNA variants ?

Thanks !

[chadn737]

I've run RNA-seq variants through Annovar. My data included known variants that we have previously confirmed and Annovar was able to correctly annotate these variants. This was also done using Arabidopsis, so I had to prepare my own databases. As long as your coordinates all match up, you shouldn't have a problem.

[swapnil2188]

As you said, you worked on known variants- I would like to know that whether you worked on Human samples ? Also, you said you did same with Arabidopsis (RNA seq data) for which you had to prepare your databases. So, I am sure that the first sample for which you had previously confirmed variants was from Human, Right ? And as they were Human so you just need to have the VCF files generated and you can go through the Annovar steps. Meaning there is no need for me to prepare my own database. Am I right ?

Thanks !

[chadn737]

I don't work on humans everything I did was in Arabidopsis, for which ANNOVAR is not originally designed, but it still works like it should when you set things up right. I looked at a variety of variant annotation programs, however, all the others I found considerably harder to adapt to use in other species. Thats why I used ANNOVAR. ANNOVAR was designed for use on human data, the databases are already packaged with it. All you should have to do is generate a VCF file and you can plug it right in without much effort.