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SnpEff_to_MutSig.R
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SnpEff_to_MutSig.R
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#!/usr/bin/env Rscript
m <- read.table('master.inc_mod.dbSnp.UNAFFECTED_INDIVIDUALS.tumor_QUAL_60.txt', comment.char="", sep="\t", header=T, fill=T)
names(m)[1] <- "patient"
m <- transform(m, patient = sprintf('P%s', patient))
names(m)[names(m)=="EFFECT"] <- "SNPEFF_EFFECT"
names(m)[names(m)=="GENE"] <- "gene"
### calculate categ
#m$categ <- 1
names(m)[names(m)=="CHROM"] <- "chr"
names(m)[names(m)=="REF"] <- "Reference_Allele"
names(m)[names(m)=="ALT"] <- "Tumor_Seq_Allele1"
m$Tumor_Seq_Allele2 <- m$Tumor_Seq_Allele1
#m$effect <- ifelse(m$Variant_Classification == "SYNONYMOUS_CODING", "silent", "nonsilent")
library(plyr)
m$effect <- revalue(
factor(m$SNPEFF_EFFECT),
c("SYNONYMOUS_CODING" = "silent",
"SYNONYMOUS_STOP" = "silent",
"INTRAGENIC" = "noncoding",
"INTRON" = "noncoding",
"UTR_3_PRIME" = "noncoding",
"UTR_5_PRIME" = "noncoding",
"EXON" = "noncoding",
"NON_SYNONYMOUS_CODING" = "nonsilent",
"FRAME_SHIFT" = "nonsilent",
"STOP_GAINED" = "nonsilent",
"CODON_CHANGE_PLUS_CODON_DELETION" = "nonsilent",
"CODON_DELETION" = "nonsilent",
"SPLICE_SITE_ACCEPTOR" = "nonsilent",
"SPLICE_SITE_DONOR" = "nonsilent",
"CODON_CHANGE_PLUS_CODON_INSERTION" = "nonsilent",
"CODON_INSERTION" = "nonsilent",
"START_LOST" = "nonsilent",
"NON_SYNONYMOUS_START" = "nonsilent",
"STOP_LOST" = "nonsilent")
)
m$Variant_Classification <- revalue(
factor(m$SNPEFF_EFFECT),
c("SYNONYMOUS_CODING" = "Silent",
"SYNONYMOUS_STOP" = "Silent",
"INTRAGENIC" = "Flank",
"INTRON" = "Intron",
"UTR_3_PRIME" = "3'UTR",
"UTR_5_PRIME" = "3'UTR",
"EXON" = "RNA",
"NON_SYNONYMOUS_CODING" = "Missense_Mutation",
"FRAME_SHIFT" = "Frame_Shift_Del",
"STOP_GAINED" = "Nonsense_Mutation",
"CODON_CHANGE_PLUS_CODON_DELETION" = "Frame_Shift_Ins",
"CODON_DELETION" = "In_Frame_Del",
"SPLICE_SITE_ACCEPTOR" = "Splice_Site",
"SPLICE_SITE_DONOR" = "Splice_Site",
"CODON_CHANGE_PLUS_CODON_INSERTION" = "Frame_Shift_Ins",
"CODON_INSERTION" = "In_Frame_Ins",
"NON_SYNONYMOUS_START" = "Translation_Start_Site",
"START_LOST" = "Translation_Start_Site",
"STOP_LOST" = "Nonstop_Mutation" )
)
#m$Variant_Classification <- ifelse(m$FUNCLASS == "SILENT", "Silent", "")
#m$Variant_Classification <- ifelse(m$FUNCLASS == "MISSENSE", "Missense_Mutation", "")
#m$Variant_Classification <- ifelse(m$FUNCLASS == "", "Frame_Shift_Del", "")
#With [the reference genome] and the Variant_Classification, Reference_Allele, and Tumor_Seq_Allele1+2 columns, "categ" can be computed.
## nuc <- ""
## if ( length(m$REF) + length(m$ALT) > 2) {
## m$categ <- "null+indel mutations"#
##} else {
## if (m$REF == "A" || m$REF == "T") {
# nuc <- "A:T"
#
# } else {
## nuc <- "C:G"
## }
## }
write.table(m, file='master.inc_mod.dbSnp.UNAFFECTED_INDIVIDUALS.tumor_QUAL_60.no_categ.txt', sep="\t", quote=F, row.names=F)