Tools or ways to find out variants in RNA seq data ?????

[swapnil2188]

I know that we can find out variants in DNA seq data using different tools(GATK, Samtools..........) but I wonder if there are any tools to find out variants in RNA seq data.

I understand the concept of RNA editing and also the ongoing debate behind it.
Please can anyone help me with how to go with this approach further ?
Also, please suggest me tools to find out variants in RNA seq data

[sdarko]

I believe that you can use GATK and samtools on RNA-Seq data.

[pbluescript]

I've run both GATK and samtools mpileup on RNA-Seq data, and I got better results with samtools. GATK is more geared towards genome SNPs, and I'm sure by playing around with the settings I could get better results with variant calling for RNA reads, but I haven't tried that yet.

[swapnil2188]

Thanks.............!!!!!!!!!! I guess this might help
I will try both GATK and samtools.

Here a found a list to analyse seq data..........

http://seqanswers.com/wiki/Software/list

I thought this might help as well.....!!!!!!!!!!!