R/get.mutect2.annotated.header.R

In shlienlab/ShlienLab.Core.SSM: Simple Somatic Mutation (SSM) library.

get.mutect2.annotated.header <- function() {
  header <- c(
    'annovar_chr',
    'annovar_start',
    'annovar_end',
    'annovar_ref',
    'annovar_alt',
    'annovar_func',
    'annovar_gene',
    'annovar_exonic_func',
    'annovar_annotation',
    'annovar_ens_func',
    'annovar_ens_gene',
    'annovar_ens_exonic_func',
    'annovar_ens_annotation',
    'annovar_dbsnp',
    'annovar_1000g',
    'annovar_esp',
    'annovar_complete_genomics',
    'annovar_cosmic',
    'annovar_clinvar',
    'annovar_exac',
    'annovar_target',
    'normal_name',
    'tumour_name',
    'gatk_filter',
    'gatk_normal_lod',
    'gatk_tumour_lod',
    'gatk_normal_genotype',
    'gatk_normal_ref_count',
    'gatk_normal_alt_count',
    'gatk_normal_depth',
    'gatk_normal_allele_fraction',
    'gatk_tumour_genotype',
    'gatk_tumour_ref_count',
    'gatk_tumour_alt_count',
    'gatk_tumour_depth',
    'gatk_tumour_allele_fraction',
    'gatk_variant_length',
    'gatk_mutation_type'
    )
  return(header)
  }