add_ID_cats_ToVCF: add_ID_cats_ToVCF

In FunGeST/Palimpsest: Package

Description

Adds Indel mutation categories to a VCF.

Usage

add_ID_cats_ToVCF(
  vcf = NULL,
  ref_fasta = NULL,
  palimpdir_man = NA,
  genome = NA,
  GRCh37 = FALSE
)

Arguments

vcf	VCF to which Indel mutation categories are to be added.
ref_fasta	Path to fasta file for reference genome of choice (e.g. hg19 genome).
palimpdir_man	Path to palimpsest directory entered manually. Must contain the "exec" folder.
genome	Taken from annotate_VCF function.
GRCh37	Logical indicating whether reference fasta file is GRCh37 (i.e. no 'chr' prefixes).

Examples

vcf <- add_ID_cats_ToVCF(vcf = vcf,ref_fasta = ref_fasta)

FunGeST/Palimpsest documentation built on June 10, 2021, 6:35 p.m.