variant_consensus: somatic_variant_consensus functions

In brucemoran/somenone: R functions required by the somenone NextFlow nf-core pipeline

somatic_variant_consensus functions

Description

Primary function to call others and produce plots, table

Usage

variant_consensus(
  germline_id,
  vep_vcf_pattern,
  raw_vcf_pattern = "raw.vcf",
  tag = "somatic_n_of_1",
  which_genome,
  included_order = NULL,
  name_callers = NULL,
  impacts = NULL
)

Arguments

germline_id	ID for germline_id sample
vep_vcf_pattern	pattern to match VEP annotated VCFs
raw_vcf_pattern	pattern to match raw unannotated, unfiltered VCFs unfiltered
tag	is a string to tag output files
which_genome	hg19 or hg38
included_order	oredering of samples for plotting
name_callers	named variant callers to use primary to random selection

Value

vector of single-letter HGVS protein IDs

brucemoran/somenone documentation built on Nov. 1, 2022, 3:56 p.m.