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 !
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 !
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