R/get_annovar_colnames.R

In Bio-Core/BioCore.Annotation: BioCore Variant Annotation Package

get_annovar_colnames <- function() {
  return(
    c(
      "Chr",
      "Start",
      "End",
      "Ref",
      "Alt",
      "Func.refGene",
      "Gene.refGene",
      "GeneDetail.refGene",
      "ExonicFunc.refGene",
      "AAChange.refGene",
      "Func.knownGene",
      "Gene.knownGene",
      "GeneDetail.knownGene",
      "ExonicFunc.knownGene",
      "AAChange.knownGene",
      "genomicSuperDups",
      "avsift",
      "cosmic70",
      "PopFreqMax",
      "1000G_ALL",
      "1000G_AFR",
      "1000G_AMR",
      "1000G_EAS",
      "1000G_EUR",
      "1000G_SAS",
      "ExAC_ALL",
      "ExAC_AFR",
      "ExAC_AMR",
      "ExAC_EAS",
      "ExAC_FIN",
      "ExAC_NFE",
      "ExAC_OTH",
      "ExAC_SAS",
      "ESP6500siv2_ALL",
      "ESP6500siv2_AA",
      "ESP6500siv2_EA",
      "CG46",
      "clinvar_20150629",
      "avsnp144",
      "snp138NonFlagged",
      "SIFT_score",
      "SIFT_pred",
      "Polyphen2_HDIV_score",
      "Polyphen2_HDIV_pred",
      "Polyphen2_HVAR_score",
      "Polyphen2_HVAR_pred",
      "LRT_score",
      "LRT_pred",
      "MutationTaster_score",
      "MutationTaster_pred",
      "MutationAssessor_score",
      "MutationAssessor_pred",
      "FATHMM_score",
      "FATHMM_pred",
      "RadialSVM_score",
      "RadialSVM_pred",
      "LR_score",
      "LR_pred",
      "VEST3_score",
      "CADD_raw",
      "CADD_phred",
      "GERP++_RS",
      "phyloP46way_placental",
      "phyloP100way_vertebrate",
      "SiPhy_29way_logOdds",
      "vcf_chr",
      "vcf_pos",
      "vcf_id",
      "vcf_ref",
      "vcf_alt",
      "vcf_qual",
      "vcf_filter",
      "vcf_info",
      "vcf_format",
      "vcf_format_sample"
    )
  )
}