Perform Tumor Mutational Burden (TMB) quantification

This function counts the total number of mutations in the object provided in input with variants. It gives in output both the total number of mutations and the number of mutations per Mb (dividing by the sequenced genomic space, extracted from the sequencing design).

callTMB(inputForTMB, genome)

Arguments

inputForTMB	a list with the following elements: sample name, filter description, design and a CollapsedVCF or data.frame object containing somatic variants
genome	human genome assembly: hg19 or hg38

Value

Returns a table with sample name, filter description, size of the sequenced genomic space and TMB expressed both as total number of mutations in the sequenced space and number of mutations per megabase

Author

Laura Fancello