Downsample a whole exome sequencing (WES) dataset to a subset only containing genes targeted in the panel

This function generates a subset of a whole exome sequencing dataset which only includes the genes of a given gene panel. This subset may then be used to simulate panel-based TMB quantification.

simulatePanel(WES, WES.design, panel.design, assembly)

Arguments

WES	a list generated by applyFilters or applyInputToTMB with variants, filter, design and sample elements.
WES.design	a GRanges object containing WES sequencing design. Used to remove off target mutations
panel.design	a GRanges object containing sequencing design of the panel tyou want to simuate. Used to subset WES.
assembly	human genome assembly: "hg19" or "hg38"

Value

Returns a GRanges object containing variants from the simulated panel, which is only those variants from WES falling in the regions targeted by the panel

Author

Laura Fancello