Provide a suitable input to the callTMB function for TMB quantification

This function reads in input an object containing mutations and generates in output a list with the following elements: filter description, an object with sequencing design and an object containing variants.

inputToTMB(vcf, design, filter)

Arguments

vcf	a CollapsedVCF object containing variants
design	a GRanges object containing WES or panel sequencing design
filter	a character string describing the type of filter previously applied to input variants

Value

Returns a list with filter description, a design object and an object containing variants, as required in input by the callTMB function

Author

Laura Fancello