Apply ecTMB in our own data

[deb0612]

Dear sir,
I cannot find a way to put my own data in the TMB model.
Is the input a maf file from Mutect2?
Do you have any suggestion?

[jorgeESSouza]

Dear sir, this is a very important point, could you produce a tutorial expeficating the use of the tool with data from vcfs, maf or txt files? without a doubt this would bring many citations to your article.

[lijingya]

Hi Jorge:
Sorry for late reply. The input for ecTMB requires MAF format. It doesn't matter which mutation caller do you use. Usually, we can get VCF file from the mutation caller and use VEP to conduct the annotation. At the end, the VEP annotated file can be converted to MAF format. Here is example nextflow code we have to convert VCF to MAF. You might find useful info there.
https://github.com/bioinform/ecTMB/blob/111b9b04d8a509c6c2daa5d4a2c003da23fb179a/inst/nf/ecTMB_refbuild.nf

Thanks

[h170607]

Hi,
The 'Example Usage' can be reproduced smoothly, but we are not clear how to analyze the actual samples and what files need to be prepared to replace the files in the instance.
Could you please give some more specific instruction?