About the calculation of the TMB?

[baike687]

Excuse me, I'm a beginner in bioinformatics.
I just wondering how the length of the human genome exon was acquired.
I see that in the script is 35.8Mb.

[PoisonAlien]

Hi,
It depends on the capture size used to target the coding regions. For example Agilent sure select kit targets ~50MB of the coding regions (exons). Earlier versions used to target ~38MB of the coding regions.

[baike687]

Thanks a lot.
And should synonymous variants be taken into the calculation of TMB?

[PoisonAlien]

Usually only non-synonymous variants with functional impact are considered for TMB. That's what maftools does by default.
But one can optionally include any kind of variants for TMB estimation (though not ideal).

[baike687]

Thanks, Anand. It's very helpful!

[PoisonAlien]

You are welcome and, all the very best.

[h170607]

Does this mean that maftools can automatically pick the appropriate mutation from the maf file to calculate the TMB without requiring us to process the maf file ourselves?
By the way, is there any suitable tool that can calculate the length of the target regions from the bed file?

[XiaoYan000]

Excuse me，
I wonder how to set the captureSize for WGS data of mice？
Looking forward to your reply

[PoisonAlien]

Hi,
You could get the gtf file and sum up all the sizes of all exonic regions.