Calculating TMB for TCGA data

Question

[Jaber]

Hi, community, I am facing a bit of a struggle to find the genomic region in Mb for the TMB calculations,

I am using the TCGA-READ data, where can I get the Mb value?

I want to calculate the TMB as follows = Total number of mutations / Mb.

I navigated Biostars' previous posts and couldn't find an answer to my question. Also, I looked up TCGA and didn't find any information regarding the Mb value (Megabase).

Is there any way I can infer the Mb from my data? Maf file of TCGA-READ I mean

I really appreciate any help you can provide.

Answer 1

[Zhenyu Zhang]

Goto GDC workflow overview page https://github.com/NCI-GDC/gdc-workflow-overview, and looking for target capture kit information at the bottom.

I remember GDC treated all TCGA WXS data as "Nextera Rapid Capture Exome v1.2", but you probably want to do API queries of GDC read group to confirm.

[Jaber]

Thank you really appreciate it

[Jaber]

Thank you for help,

However, I could not identify the Mb for TCAG-READ, where should I do API queries to identify which kit they used for this dataset?

[Zhenyu Zhang]

https://github.com/NCI-GDC/gdc-workflow-overview/blob/04b73036022ff1f53921dff5ef3b1b638b8ecfcd/gdc_target_capture_kit_size.tsv#L4

You can use this value. Just to clarify, this is not the exact capture kit TCGA has used, just GDC uses this as the default. TCGA has used like 40+ different kit/combinations, and sometimes the same file was generated of read groups from different kits.