How to get the number of RNA reads for mutations of exome-seq?
Hi.
I am studying how do mutations have influence on protein quantification in mass spectrometry.
I called variants from exome-seq data and made it vcf format.
In addition, I have RNA-seq data and would like to get two kinds of information.
One is the number of RNA reads supporting the identified mutation based on exome-seq. The other is the number of RNA reads that don't provide evidence for the mutation.
Does GATK provide these kinds of information?
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