I'd like to supplement variant calls in WGS with RNA-Seq data. Essentially, I would like to use the additional information in RNA-Seq to provide a "tie-breaker" of sorts for SNVs which are on the border of being significant within WGS. If I have a position which is almost a SNV at the genomic level (say 20 reference and 4 variant reads), and I see the same variant reads at the RNA level, I am inclined to believe it is a SNV as opposed to some random sequencing error. Is anyone aware of a tool which can incorporate RNA-Seq like this?
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You can make vcfs for your WGS, and a vcf for your RNAseq, and there are a bunch of programs that you can use to compare two vcfs.
Or, if both are aligned to genome, you can call SNPs on both together (like with samtools mpileup), and look for SNPs that are in both. -
The issue with that is it succumbs to the issue that we are limiting the information available. I'm not looking for the intersection/union of SNVs, but for a more bayesian approach that adjusts the prior likelihood based on RNA-Seq evidence.Comment
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