Read a VCF into an MAF-like table

This function loads VCF files into MAF-like tables. A Tumor_Sample_Barcode column is added, and the contents of the POS/REF/ALT fields are converted to match the style used by MAF files for Start_Position/Reference_Allele/Tumor_Seq_Allele2. The VCF file should represent high-confidence somatic variant calls for a single tumor sample.

Usage

vcfs_to_maf_table(vcfs, sample_ids)

Arguments

vcfs

Vector of VCF file paths, or a list of VCF-like data.tables, or a single data.table.

sample_ids

Identifiers to populate Tumor_Sample_Barcode, one per VCF.

Value

A single data.table with MAF-style fields, suitable for use with cancereffectsizeR.