Merged Canvas and Manta VCF parsing function

Parse a VCF file merged from Canvas and Manta, which stores a list of segments with absolute CNA events, and tumour purity.

The obtained data, together with mutation calls (loaded elsewhere) can be used to call function autofit.

load_VCF_Canvas_Manta(file)

Arguments

file

VCF filename.

Value

A named list with the calls and tumour purity.

Examples

# not run
if (FALSE) {
 load_VCF_Canvas_Manta("Myfile.vcf")
}