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bioinfo-pf-curie / TMB

Tumor Mutational Burden
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How to use for WGS data #13

Closed praveenraj2018 closed 1 year ago

praveenraj2018 commented 1 year ago

Very nice to see a tool with a comprehensive list of parameters!!

I am a little unclear on how to use this for whole-genome data. Should we use --effGenomeSize or --bed file or both? What do you recommend and a typical example usage from your validation experiments? This would be very useful to know and if possible include it in the documentation.

thanks!

tomgutman commented 1 year ago

Hello,

This tool was primarily developed and tested for WES and panels. We have never used it for WGS. But it is totally usable for this type of data. I would advise to use --effGenomeSize with the size of the reference genome used. For the parameters I would advise to include coding, non coding and splicing variants.

I hope it helps

Tom

praveenraj2018 commented 1 year ago

Thanks. I will certainly try this out.