diff --git a/pcgr/config.py b/pcgr/config.py
index 486de4bb..3b314cc9 100644
--- a/pcgr/config.py
+++ b/pcgr/config.py
@@ -133,6 +133,7 @@ def create_config(arg_dict, workflow = "PCGR"):
         conf_options['molecular_data']['fname_cna_tsv'] = "None"
         conf_options['molecular_data']['fname_expression_tsv'] = "None"
         conf_options['molecular_data']['fname_expression_outliers_tsv'] = "None"
+        conf_options['molecular_data']['fname_maf_tsv'] = "None"
         #conf_options['molecular_data']['fname_expression_csq_tsv'] = "None"
         conf_options['molecular_data']['fname_expression_similarity_tsv'] = "None"
         conf_options['molecular_data']['fname_tmb_tsv'] = "None"
diff --git a/pcgr/main.py b/pcgr/main.py
index 3d2a6888..3134f058 100755
--- a/pcgr/main.py
+++ b/pcgr/main.py
@@ -297,6 +297,8 @@ def run_pcgr(input_data, output_data,conf_options):
         conf_options['output_prefix'] = output_prefix
         conf_options['molecular_data']['fname_mut_vcf'] = output_vcf
         conf_options['molecular_data']['fname_mut_tsv'] = output_pass_tsv_gz
+        if conf_options['other']['vcf2maf'] == 1:
+            conf_options['molecular_data']['fname_maf_tsv'] = output_maf
         if conf_options['somatic_snv']['tmb']['run'] == 1:
             conf_options['molecular_data']['fname_tmb_tsv'] = tmb_fname
         if not input_cna == 'None':
diff --git a/pcgrr/NAMESPACE b/pcgrr/NAMESPACE
index 961e4d09..5381731a 100644
--- a/pcgrr/NAMESPACE
+++ b/pcgrr/NAMESPACE
@@ -28,6 +28,7 @@ export(exclude_non_chrom_variants)
 export(expand_biomarker_items)
 export(export_quarto_evars)
 export(filter_eitems_by_site)
+export(filter_maf_file)
 export(filter_read_support)
 export(generate_annotation_link)
 export(generate_report)
diff --git a/pcgrr/R/input_data.R b/pcgrr/R/input_data.R
index 5586a64f..5910db58 100644
--- a/pcgrr/R/input_data.R
+++ b/pcgrr/R/input_data.R
@@ -221,6 +221,11 @@ load_somatic_snv_indel <- function(
         dplyr::filter(
           .data$SOMATIC_CLASSIFICATION == "SOMATIC")
 
+      ## filter also MAF file if provided
+      pcgrr::filter_maf_file(
+        callset = callset,
+        settings = settings)
+
       ## Issue warning if clinically actionable variants are filtered
       ## with current filtering settings
       n_actionable_filtered <-
diff --git a/pcgrr/R/maf.R b/pcgrr/R/maf.R
new file mode 100644
index 00000000..efbd0cb0
--- /dev/null
+++ b/pcgrr/R/maf.R
@@ -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)
+}
diff --git a/pcgrr/man/filter_maf_file.Rd b/pcgrr/man/filter_maf_file.Rd
new file mode 100644
index 00000000..6a3a3b81
--- /dev/null
+++ b/pcgrr/man/filter_maf_file.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/maf.R
+\name{filter_maf_file}
+\alias{filter_maf_file}
+\title{Function that takes a MAF file generated with vcf2maf
+and filters out variants that are presumably germline (tumor-only run)}
+\usage{
+filter_maf_file(callset, settings)
+}
+\arguments{
+\item{callset}{Callset with pre-processed somatic SNV/InDel variants}
+
+\item{settings}{PCGR run/configuration settings}
+}
+\description{
+Function that takes a MAF file generated with vcf2maf
+and filters out variants that are presumably germline (tumor-only run)
+}