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Tumor Mutation Burden

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4.1 years ago

atheeth14 • 0

Hi,

I'm a data scientist trying to perform predictive modeling on clinical trial patients based on TMB. However, the data provided was raw fast-q files. We have succeeded in generating BAM alignment files. How do I measure non-synonymous mutations per Mb in these files? Is there any R package I can use for the same?

Tumor Mutation Burden alignment RNA-Seq • 1.1k views

ADD COMMENT • link updated 4.1 years ago by GenoMax 141k • written 4.1 years ago by atheeth14 • 0

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You will have to do variant calling (please google variant callers, there are plenty of them) followed by variant annotation. Tools like VEP, Annovar, snpeff come to mind. Then filter for non-syn. variants. No, there is no all-in-one tool in R that does that directly from BAM files.

ADD REPLY • link 4.1 years ago by ATpoint 81k

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Prior thread that may be of interest:
How to calculate Tumor Mutation Burden (TMB) for TCGA samples

ADD REPLY • link 4.1 years ago by GenoMax 141k

score 0 · Answer 1 · 2020-03-05

As I mentioned in my other answer ( A: Tool or R package for computing Tumor Mutational Burden? ), Atheeth, it is easy to do this manually. Keep in mind that there is no 'definitive' definition of TMB.

You could use the output of the programs mentioned by ATpoint, and/or take suggestions from here: A: pathogenicity predictors of cancer mutations

In R, you may find it easy to summarise the data by utilising the GenomicRanges framework.