Minimum alternative allele depth

[HMR24]

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]

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