Filter truncating variants in tumor suppressors

This function removes from the input vcf truncating variants in tumor suppressor genes

filterTruncatingTumorSuppr(vcf, assembly, tsList)

Arguments

vcf	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 (<https://bioinfo.uth.edu/TSGene/>) is used.

Value

Returns a data.frame object with those variants which do not represent truncating mutations in tumor suppressors

Author

Laura Fancello