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properly filter MAF output in tumor-only mode
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| #' Function that takes a MAF file generated with vcf2maf | ||
| #' and filters out variants that are presumably germline (tumor-only run) | ||
| #' | ||
| #' @param callset Callset with pre-processed somatic SNV/InDel variants | ||
| #' @param settings PCGR run/configuration settings | ||
| #' | ||
| #' @export | ||
| filter_maf_file <- function(callset, settings) { | ||
|
|
||
| ## check if vcf2maf is TRUE | ||
| if (as.logical(settings[['conf']][['other']][['vcf2maf']]) == FALSE) { | ||
| return(0) | ||
| } | ||
|
|
||
| filtered_vars_maf_like <- data.frame() | ||
|
|
||
| if("variant" %in% names(callset)) { | ||
| if(NROW(callset[['variant']]) == 0) { | ||
| return(0) | ||
| } | ||
|
|
||
| pcgrr::log4r_info(paste0( | ||
| "Updating MAF file with filtered somatic SNV/InDels")) | ||
|
|
||
| if(all(c("CHROM", | ||
| "POS", | ||
| "REF", | ||
| "ALT") %in% colnames(callset[['variant']]))) { | ||
| filtered_vars_maf_like <- callset[['variant']] |> | ||
| dplyr::select(c("CHROM", "POS", "REF", "ALT")) |> | ||
| dplyr::mutate(Tumor_Seq_Allele1 = dplyr::case_when( | ||
| nchar(.data$REF) > 1 & | ||
| nchar(.data$ALT) == 1 & | ||
| substr(.data$REF, 1, 1) == .data$ALT ~ substr(.data$REF, 2, nchar(.data$REF)), | ||
| nchar(.data$ALT) > 1 & | ||
| nchar(.data$REF) == 1 & | ||
| substr(.data$ALT, 1, 1) == .data$REF ~ "-", # insertion | ||
| TRUE ~ .data$REF | ||
| )) |> | ||
| dplyr::mutate(Tumor_Seq_Allele2 = dplyr::case_when( | ||
| nchar(.data$REF) > 1 & | ||
| nchar(.data$ALT) == 1 & | ||
| substr(.data$REF, 1, 1) == .data$ALT ~ "-", | ||
| nchar(.data$ALT) > 1 & | ||
| nchar(.data$REF) == 1 & | ||
| substr(.data$ALT, 1, 1) == .data$REF ~ substr(.data$ALT, 2, nchar(.data$ALT)), | ||
| TRUE ~ .data$ALT | ||
| )) |> | ||
| dplyr::mutate(Variant_Type = dplyr::case_when( | ||
| nchar(.data$REF) == 1 & | ||
| nchar(.data$ALT) == 1 ~ "SNP", | ||
| nchar(.data$REF) > 1 & | ||
| nchar(.data$ALT) == 1 ~ "DEL", | ||
| nchar(.data$ALT) > 1 & | ||
| nchar(.data$REF) == 1 ~ "INS", | ||
| TRUE ~ "MNP" | ||
| )) |> | ||
| dplyr::mutate( | ||
| Chromosome = .data$CHROM, | ||
| Start_Position = dplyr::case_when( | ||
| .data$Variant_Type == "DEL" & | ||
| substr(.data$REF, 1, 1) == .data$ALT ~ .data$POS + 1, | ||
| TRUE ~ .data$POS | ||
| ) | ||
| ) |> | ||
| dplyr::select( | ||
| c("Chromosome", | ||
| "Start_Position", | ||
| "Tumor_Seq_Allele1", | ||
| "Tumor_Seq_Allele2", | ||
| "Variant_Type") | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| maf_data_unfiltered <- data.frame() | ||
| maf_data_header <- NULL | ||
|
|
||
| ## check if unfiltered MAF file exists and read it - if not, return 0 | ||
| if (file.exists(settings[['molecular_data']][['fname_maf_tsv']])) { | ||
| if(!(file.size(settings[['molecular_data']][['fname_maf_tsv']]) == 0)) { | ||
| maf_data_header <- readLines( | ||
| settings[['molecular_data']][['fname_maf_tsv']], n = 1) | ||
|
|
||
| maf_data_unfiltered <- readr::read_tsv( | ||
| settings[['molecular_data']][['fname_maf_tsv']], | ||
| show_col_types = F, col_names = T, | ||
| comment = "#", na = "" | ||
| ) | ||
| } else { | ||
| pcgrr::log4r_warn("MAF file is empty - no filtering will be performed") | ||
| return(0) | ||
| } | ||
| } | ||
|
|
||
| if(NROW(maf_data_unfiltered) > 0 & | ||
| NROW(filtered_vars_maf_like) > 0) { | ||
| if(all(c("Chromosome", | ||
| "Start_Position", | ||
| "Tumor_Seq_Allele1", | ||
| "Tumor_Seq_Allele2", | ||
| "Variant_Type") %in% colnames(maf_data_unfiltered)) & | ||
| all(c("Chromosome", | ||
| "Start_Position", | ||
| "Tumor_Seq_Allele1", | ||
| "Tumor_Seq_Allele2", | ||
| "Variant_Type") %in% colnames(filtered_vars_maf_like))) { | ||
| maf_data_filtered <- maf_data_unfiltered |> | ||
| dplyr::semi_join( | ||
| filtered_vars_maf_like, | ||
| by = c("Chromosome", "Start_Position", | ||
| "Tumor_Seq_Allele1", "Tumor_Seq_Allele2", | ||
| "Variant_Type") | ||
| ) | ||
|
|
||
| if(!is.null(maf_data_header) & | ||
| NROW(maf_data_filtered) > 0) { | ||
| file.remove(settings[['molecular_data']][['fname_maf_tsv']]) | ||
| writeLines(maf_data_header, | ||
| settings[['molecular_data']][['fname_maf_tsv']]) | ||
| options(scipen = 999) | ||
| readr::write_tsv( | ||
| maf_data_filtered, | ||
| settings[['molecular_data']][['fname_maf_tsv']], | ||
| append = TRUE, col_names = T, quote = "none", na = "") | ||
| } | ||
| } | ||
| } | ||
|
|
||
| return(0) | ||
| } |
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