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