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Tumor Mutation Burden

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
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updated by GenoMax GenoMax • written by atheeth14 • atheeth14

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.

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written by ATpoint ATpoint

1 answer

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.

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written by Kevin Blighe Kevin Blighe

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