Merging variant calls of whole exome and RNA-seq

Question

[Saad Khan]

Hi,

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.

Thanks!

Answer 1

[Omics data mining]

Hi , You can go through this paper https://github.com/aradenbaugh/radia

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

I hope , this can work for you.

[Saad Khan]

@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.