Calculate TMB from BAM file

Question

[Manuel Sokolov Ravasqueira]

Given BAM file and its BAI file, how can I calculate the TMB for the patient? This bam file is the result of target sequencing, so I would like to calculate the TMB over the genomic region of interest. Is there any package or software that can do this?

Answer 1

[Trivas]

Tumour mutation burden is calculated by counting the number of somatic mutations above a threshold frequency in data derived from whole genome sequencing, whole exome sequencing (WES) or panel sequencing and dividing by the size of the target region [20]

https://bmccancer.biomedcentral.com/articles/10.1186/s12885-022-09897-3#:~:text=Tumour%20mutation%20burden%20is%20calculated,the%20target%20region%20%5B20%5D.