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Readin only these selected columns: Gene name GENOMIC_MUTATION_ID Mutation AA Mutation Description Mutation genome position SNP FATHMM prediction HGVSG

cosm = data.table::fread(cmd = "zcat CosmicCompleteTargetedScreensMutantExport.tsv.gz | cut -f 1,17,21,22,26,28,30,40 | sed 1d | sort -k1,2", header = FALSE) csom = cosm[!V2 %in% ""] csom = csom[!V4 %in% "Substitution - coding silent"] #Remove silent variants csom = csom[!V4 %in% ""] #Remove vars with no sub. type variants csom[, id := paste0(V2, ":", V3)] csom = csom[!duplicated(id)] #Remove dup entries csom = csom[!V4 %in% "Unknown"]

csom = csom[!V6 %in% "y"] #Remove SNPs csom = csom[V7 %in% "PATHOGENIC"] #Keep pathogenic vars

Small func to convert chr:10-11 to chr start end

loci2df = function(loci){ chr = as.character(unlist(data.table::tstrsplit(x = loci, spli = ":", keep = 1))) start = unlist(data.table::tstrsplit(x = unlist(data.table::tstrsplit(x = loci, split = ":", keep = 2)), split = "-", keep = 1)) start = as.numeric(as.character(gsub(pattern = ",", replacement = "", x = as.character(start)))) end = unlist(data.table::tstrsplit(x = unlist(data.table::tstrsplit(x = loci, split = ":", keep = 2)), split = "-", keep = 2)) end = as.numeric(as.character(gsub(pattern = ",", replacement = "", x = as.character(end)))) data.table::data.table(chr, start, end) }

locdf = loci2df(csom$V5) locdf$type = csom$V4 locdf$Hugo_Symbol = csom$V1 locdf$HGVSp = csom$V3 locdf$COSMIC_ID = csom$V2

locdf$conv = substr(x = csom$V8, start = nchar(csom$V8)-2, stop = nchar(csom$V8)) locdf$ref = substr(x = locdf$conv, 1, 1) locdf$alt = substr(x = locdf$conv, 3, 3) locdf = locdf[,.(chr, start, ref, alt, Hugo_Symbol, type, HGVSp, COSMIC_ID)] locdf = locdf[!chr %in% 24] #Remove chrY locdf = locdf[order(Hugo_Symbol)][!duplicated(COSMIC_ID)] locdf[,type := gsub(pattern = "Substitution - ", replacement = "", x = type)] locdf=locdf[order(as.numeric(chr), start)] data.table::fwrite(locdf, "COSMIC_nsyn_GRCh37.tsv", sep="\t", col.names=FALSE)