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.
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written
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Jaber •
1 answer
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.
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.
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