Filters variants according to input arguments

This function calls different filtering functions on the input vcf object according to the input arguments and gives in output a list with the three elements: an object containg variants which passed the filter, a character string describing the applied filter (if any) and an object containing the sequencing design

callFilters(
  vcf,
  assembly,
  design,
  vaf.cutoff,
  remove.cancer,
  remove.nonexonic,
  tsList,
  variantType
)

Arguments

vcf	CollapsedVCF object
assembly	human genome assembly: hg19 or hg38
design	a GRanges object containing WES or panel design
vaf.cutoff	minimum value of variant allele frequency accepted
remove.cancer	logical value 'TRUE' or 'FALSE' indicating whether or not to remove cancer variants, which is variants described in COSMIC or truncating mutations in tumor suppressors
remove.nonexonic	logical value 'TRUE' or 'FALSE' indicating whether or not to remove SNV mapped in non exonic regions
tsList	path to file containing list of tumor suppressors. If not provided a list of 1217 tumor suppressors from the TSgene2 database (<https://bioinfo.uth.edu/TSGene/>) is used.
variantType	type of variant to remove: synonymous, frameshift or nonsense

Value

Returns a list with the following elements: a GRanges, CollapsedVCF, data.frame object containing variants passing the filter, a charcater string describing applied filter (if any), a GRanges or character vector with the sequencing design,.

Author

Laura Fancello