how to calculate TMB from call stats file

Question

[rotemkat]

Hi, I want calculate the TMB for each sample in a cohort i'm using. I have the mutations data in call stats file. I know that for the calculation i should know the number of non-synonymous somatic, coding, base substitution, per megabase of genome examined, but i'm not sure what data informs about the size of Mb?

Thanks in advance

[igor]

You have to find out what kind of sequencing was done. Is it whole genome or exome? If exome, which panel was used?

[rotemkat]

it was actually neither - this is RNA-seq data.

[igor]

You can use GATK CallableLoci to get the number of covered bases.