Entering edit mode
10 weeks ago
tanbiswas6 ▴ 10
I've tumor-normal WES data and I've analyzed data using GATK-Mutect2 pipeline to call somatic mutations. Now can anyone let me know hoe to calculate tumor mutation burden or mutation rate of my samples? I'm not able to find out the base pairs covered in my data. If so, then also I can divide total no of mutations with bases covered. But do not know from where I'll get the bases covered.
Also, is there any tool that can analyze TMB?
I just published a post on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the approach described in a recent paper. This was part of the thesis work of a student of mine. We are not 100% sure that this is the right way to do it, feedback is welcome.