annotate_VCF: annotate_VCF
In FunGeST/Palimpsest: Package

Description Usage Arguments Value Examples

Function to add strand, gene and COSMIC mutation category annotations to a VCF. This function can take a long time depending on the number of mutations and how many of the annotation options you have selected. Please be patient!

annotate_VCF(
  vcf = vcf,
  add_strand_and_SBS_cats = T,
  add_DBS_cats = T,
  add_ID_cats = F,
  ref_fasta = NULL,
  ref_genome = BSgenome.Hsapiens.UCSC.hg19,
  palimpdir = NA,
  GRCh37_fasta = FALSE
)

`vcf`	Input VCF to annotate.
`add_strand_and_SBS_cats`	Logical indicating whether or not strand, gene and SBS category annotations are to be added (defaults to TRUE).
`add_DBS_cats`	Logical indicating whether or not DBS category annotations are to be added (defaults to TRUE).
`add_ID_cats`	Logical indicating whether or not Indel category annotations are to be added (defaults to FALSE). Unfortunately Indel mutation categories cannot be added to the VCF in Windows, as this R function calls a python script. Please run this step in a unix environment (Mac/Linux etc.).
`ref_fasta`	File path to FASTA file compatable with input VCF positions and chromosomes. Only required when add_ID_cats = TRUE. The latest reference genomes in FASTA format can be downloaded here
`ref_genome`	Name of reference genome object. For hg19 data we use the BSgenome.Hsapiens.UCSC.hg19 object, which is loaded into the local environment by library(BSgenome.Hsapiens.UCSC.hg19). Use library(BSgenome.Hsapiens.UCSC.hg38) as appropirate.
`palimpdir`	If you received a filepath error when adding indel categories, set this parameter as a filepath to the location of the Palimpsest package directory that you downloaed from our GitHub
`GRCh37_fasta`	If you received a VCF/FASTA error when adding indel categories, and you are working with GRCh37 data (or your hg19 FASTA has no 'chr' prefixes) set to TRUE.