Question: Merging variant calls of whole exome and RNA-seq
gravatar for Saad Khan
8 months ago by
Saad Khan370
United States
Saad Khan370 wrote:


I have many samples for which I have whole-exome and corresponding RNA-seq data I have already done GATK variant calling using their best practices and recommendations. Now I would like to merge the variants from the two approaches. I know the merging may not be straightforward because of RNA-seq editing and other factors but I was wondering if any one knows of a published method/approach that does this.


indels rna-seq variants gatk snvs • 311 views
ADD COMMENTlink modified 8 months ago by archie90 • written 8 months ago by Saad Khan370
gravatar for archie
8 months ago by
archie90 wrote:

Hi , You can go through this paper

where authors mentioned use of DNA and RNA snps but it is tumor specific.

I hope , this can work for you.

ADD COMMENTlink written 8 months ago by archie90

@archie This probably does not do what I want. I only need to merge the RNA and exome vcf file so that I can make a consensus fasta file from it using FastaAlternateReferenceMaker in GATK.

ADD REPLYlink modified 8 months ago • written 8 months ago by Saad Khan370
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