Remove cancer variants

This function removes from the vcf dataset those variants defined as pathogenic (cancer) in COSMIC or truncating variants in tumor suppressor genes.

removeCancerVariants(vcf, assembly, tsList)

Arguments

vcf	a CollapsedVCF object containing variants
assembly	human genome assembly: hg19 or hg38
tsList	path to file containg list of tumor suppressors. If not provided a list of 1217 tumor suppressors from the TSgene2 database is used.

Value

Returns a data.frame object containing only those variants which passed the filter

Author

Laura Fancello