A simple R script to convert an ICGC simple mutations file into the TCGA MAF format for re-annotation with maf2maf (see vcf2maf)

icgc_to_maf.R

suppressPackageStartupMessages({
  library(readr)
  library(dplyr)
})

maf_cols <- c(
  "Hugo_Symbol","Entrez_Gene_Id","Center","NCBI_Build","Chromosome","Start_Position",
  "End_Position","Strand","Variant_Classification","Variant_Type","Reference_Allele",
  "Tumor_Seq_Allele1","Tumor_Seq_Allele2","dbSNP_RS","dbSNP_Val_Status","Tumor_Sample_Barcode",
  "Matched_Norm_Sample_Barcode","Match_Norm_Seq_Allele1","Match_Norm_Seq_Allele2",
  "Tumor_Validation_Allele1","Tumor_Validation_Allele2","Match_Norm_Validation_Allele1",
  "Match_Norm_Validation_Allele2","Verification_Status","Validation_Status","Mutation_Status",
  "Sequencing_Phase","Sequence_Source","Validation_Method","Score","BAM_File","Sequencer",
  "Tumor_Sample_UUID","Matched_Norm_Sample_UUID")

args = commandArgs(trailingOnly=TRUE)
input <- args[1]
output <- args[2]
# input <- "simple_somatic_mutation.open.MALY-DE.tsv"
# output <- "mutations.MALY-DE.tsv"

raw_mutations <- read_tsv(input)

mutations <- raw_mutations %>%
  transmute(NCBI_Build = assembly_version,
            Chromosome = chromosome,
            Start_Position = chromosome_start,
            End_Position = chromosome_end,
            Strand = "+",
            Reference_Allele = reference_genome_allele,
            Tumor_Seq_Allele1 = mutated_from_allele,
            Tumor_Seq_Allele2 = mutated_to_allele,
            Tumor_Sample_Barcode = submitted_sample_id,
            Matched_Norm_Sample_Barcode = submitted_matched_sample_id,
            Variant_Type =  ifelse(mutation_type == "single base substitution", "SNP",
                            ifelse(mutation_type == "deletion of <=200bp", "DEL",
                            ifelse(mutation_type == "insertion of <=200bp", "INS", "Other")))) %>%
  filter(Variant_Type != "Other")

remaining_cols <- setdiff(maf_cols, colnames(mutations))

for (col in remaining_cols) {
  mutations[, col] <- NA
}

mutations <- mutations[maf_cols]

write_tsv(mutations, output, na = "")