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bioinfo-pf-curie / TMB

Tumor Mutational Burden
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Minimum alternative allele depth #10

Open HMR24 opened 2 years ago

HMR24 commented 2 years ago

Hi I work within the National Health Service (NHS) in the UK and have used the TMB tool within a piece of in-house research work into the utility of TMB in lung patients. I don't have a clear understanding of the importance of the minimum alternative allele depth within the TMB calculation; can you provide more information regarding how the setting of this parameter relates to the TMB score? I used the default value of '2' for this parameter in my study. Thank you, Helen

tomgutman commented 2 years ago

Hi The minimum alternative allele depth is linked to the depth of the variant. The higher the coverage, the higher the confidence for this variant. Below a threshold and depending on your data type, variant can be suspicious. Moreover, the VAF is also taking in count this information. Because we wanted to provide a tool as flexible as possible we provide this option, although it's not directly linked to the TMB score. Setting up a higher --minAltDepth threshold might filter variant not well covered and reduce overall TMB score. I hope it helps Tom