diff --git a/DESCRIPTION b/DESCRIPTION
index 23e352e..2fe19a0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.9.10
+Version: 1.9.11
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",
diff --git a/NEWS.md b/NEWS.md
index c43a913..d9e4c3c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,13 @@
+## CHANGES IN VERSION 1.9.11
+
+### New features
+* The `rmv_chrPrefix` parameter in `format_sumstats()` has been replaced with
+the new `chr_style` parameter, which allows users to specify their desired
+chromosome name style. The supported chromosome styles are "NCBI", "UCSC", "dbSNP",
+and "Ensembl" with "Ensembl" being the default.
+* `check_chr()` now automatically removes all SNPs with nonstandard CHR entries
+(anything other than 1-22, X, Y, and MT in the Ensembl naming style).
+
 ## CHANGES IN VERSION 1.9.10
 
 ### Bug fix
diff --git a/R/check_chr.R b/R/check_chr.R
index 0a1d1e0..00ff4fc 100644
--- a/R/check_chr.R
+++ b/R/check_chr.R
@@ -1,84 +1,90 @@
-#' Ensure all SNPs on specified chromosomes are removed
+#' Standardize the CHR column
 #'
+#' Maps chromosome names to the default Ensembl/NCBI naming style and removes
+#' SNPs with nonstandard CHR entries. Optionally, also removes SNPs on
+#' user-specified chromosomes.
+#'
+#' @param sumstats_dt data.table with summary statistics
+#' @param log_files list of locations for all log files
+#' @param check_save_out list of parameters for saved files
 #' @inheritParams format_sumstats
-#' @param log_files list of log file locations
-#' @return list containing sumstats_dt, the modified summary statistics data
-#' table object and the log file list
+#' @return list containing the updated summary statistics data.table and the
+#'   updated log file locations list
 #' @keywords internal
 check_chr <- function(sumstats_dt,
-                      path,
-                      rmv_chr,
-                      log_folder_ind,
+                      log_files,
                       check_save_out,
-                      tabix_index,
+                      rmv_chr,
                       nThread,
-                      log_files,
-                      make_uppercase = TRUE,
-                      rmv_chrPrefix = TRUE) {
-    CHR <- NULL
-    # If CHR present and user specified chromosome to have SNPs removed
-    col_headers <- names(sumstats_dt)
-    if ("CHR" %in% col_headers && !is.null(rmv_chr)) {
+                      tabix_index,
+                      log_folder_ind) {
+  CHR <- NULL
 
-        ### Sometimes X is labeled as 23
-        sumstats_dt[, CHR := gsub("23", "X", CHR)]
+  # The CHR column needs to be a character vector for gsub substitution to work
+  sumstats_dt[, CHR := as.character(CHR)]
 
-        #### Remove chr prefix uppercase ####
-        if (rmv_chrPrefix) {
-            message("Removing 'chr' prefix from CHR.")
-            sumstats_dt[, CHR := gsub("chr", "", CHR, ignore.case = TRUE)]
-            rmv_chr <- gsub("chr", "", rmv_chr, ignore.case = TRUE)
-        }
-        #### Make all CHR uppercase ####
-        if (make_uppercase) {
-            message("Making X/Y/MT CHR uppercase.")
-            sumstats_dt[, CHR := gsub("x|23", "X", CHR)]
-            sumstats_dt[, CHR := gsub("y", "Y", CHR)]
-            sumstats_dt[, CHR := gsub("mt", "MT", CHR)]
-        }
+  ### Reformat chromosome names according to the default style (Ensembl/NCBI)
+  # Remove the "chr" prefix
+  sumstats_dt[, CHR := gsub("chr", "", CHR, ignore.case = TRUE)]
+  # Remove the "ch" prefix
+  sumstats_dt[, CHR := gsub("ch", "", CHR, ignore.case = TRUE)]
+  # Rename "23" to "X"
+  sumstats_dt[, CHR := gsub("23", "X", CHR)]
+  # Rename "M" to "MT"
+  sumstats_dt[, CHR := gsub("M", "MT", CHR, ignore.case = TRUE)]
+  # Make all chromosome names uppercase
+  sumstats_dt[, CHR := toupper(CHR)]
 
-        # check for chromosomes to be removed
-        ### Standardise chromosomes specified
-        rmv_chr <- toupper(rmv_chr)
-        if (any(rmv_chr %in% unique(sumstats_dt$CHR))) {
-            num_bad_ids <- nrow(sumstats_dt[CHR %in% rmv_chr, ])
-            msg <- paste0(
-                formatC(num_bad_ids, big.mark = ","),
-                " SNPs are on chromosomes ",
-                paste(rmv_chr, collapse = ", "),
-                " and will be removed"
-            )
-            message(msg)
-            # If user wants log, save it to there
-            if (log_folder_ind) {
-                name <- "chr_excl"
-                name <- get_unique_name_log_file(
-                    name = name,
-                    log_files = log_files
-                )
-                write_sumstats(
-                    sumstats_dt = sumstats_dt[CHR %in% (rmv_chr), ],
-                    save_path =
-                        paste0(
-                            check_save_out$log_folder,
-                            "/", name,
-                            check_save_out$extension
-                        ),
-                    sep = check_save_out$sep,
-                    tabix_index = tabix_index,
-                    nThread = nThread
-                )
-                log_files[[name]] <-
-                    paste0(
-                        check_save_out$log_folder, "/", name,
-                        check_save_out$extension
-                    )
-            }
-            # remove rows on these chromosomes
-            sumstats_dt <- sumstats_dt[!CHR %in% (rmv_chr), ]
-        }
-        return(list("sumstats_dt" = sumstats_dt, "log_files" = log_files))
-    } else {
-        return(list("sumstats_dt" = sumstats_dt, "log_files" = log_files))
+  ### Remove rows with nonstandard CHR entries
+  standard_chrs <- c(1:22, "X", "Y", "MT")
+  nonstandard_rows <- which(!(sumstats_dt$CHR %in% standard_chrs))
+  if (length(nonstandard_rows) > 0L) {
+    message("Removing ",
+            formatC(length(nonstandard_rows), big.mark = ","),
+            " SNPs with nonstandard CHR entries.")
+  }
+
+  ### Remove SNPs on user-specified chromosomes, if requested
+  rmv_chr_rows <- c()
+  if (!is.null(rmv_chr)) {
+    # Check for chromosomes to be removed
+    rmv_chr_rows <- which(sumstats_dt$CHR %in% rmv_chr)
+
+    if (length(rmv_chr_rows) > 0L) {
+      message(
+        formatC(length(rmv_chr_rows), big.mark = ","),
+        " SNPs are on chromosomes ",
+        paste(rmv_chr, collapse = ", "),
+        " and will be removed."
+      )
     }
+  }
+
+  # Vector of row numbers for all removed SNPs
+  all_removed_rows <- sort(unique(c(nonstandard_rows, rmv_chr_rows)))
+
+  ### Save a log of removed SNPs if the user wants it
+  if (log_folder_ind && (length(all_removed_rows) > 0L)) {
+    name <- "chr_excl"
+    name <- get_unique_name_log_file(name = name,
+                                     log_files = log_files)
+    save_path <- paste0(check_save_out$log_folder,
+                        "/",
+                        name,
+                        check_save_out$extension)
+
+    write_sumstats(
+      sumstats_dt = sumstats_dt[all_removed_rows],
+      save_path = save_path,
+      sep = check_save_out$sep,
+      tabix_index = tabix_index,
+      nThread = nThread
+    )
+    log_files[[name]] <- save_path
+  }
+
+  # Remove the SNPs identified above, if any
+  sumstats_dt <- sumstats_dt[!all_removed_rows]
+
+  return(list(sumstats_dt = sumstats_dt, log_files = log_files))
 }
diff --git a/R/format_sumstats.R b/R/format_sumstats.R
index 8a9625b..86e7bf3 100644
--- a/R/format_sumstats.R
+++ b/R/format_sumstats.R
@@ -48,7 +48,7 @@
 #' @param chain_source source of the chain file to use in liftover, if converting
 #' genome build ("ucsc" or "ensembl"). Note that the UCSC chain files require a
 #' license for commercial use. The Ensembl chain is used by default ("ensembl").
-#' @param convert_small_p Binary, should non-negative 
+#' @param convert_small_p Binary, should non-negative
 #' p-values <= 5e-324 be converted to 0?
 #' Small p-values pass the R limit and can cause errors with LDSC/MAGMA and
 #' should be converted. Default is TRUE.
@@ -56,10 +56,10 @@
 #' P-values >1 should not be possible and can cause errors with LDSC/MAGMA and
 #' should be converted. Default is TRUE.
 #' @param convert_neg_p Binary, should p-values <0 be converted to 0?
-#' Negative p-values should not be possible and can cause errors 
+#' Negative p-values should not be possible and can cause errors
 #' with LDSC/MAGMA and should be converted. Default is TRUE.
-#' @param compute_z Whether to compute Z-score column. Default is FALSE. This 
-#' can be computed from Beta and SE with (Beta/SE) or P 
+#' @param compute_z Whether to compute Z-score column. Default is FALSE. This
+#' can be computed from Beta and SE with (Beta/SE) or P
 #' (Z:=sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE))).
 #' **Note** that imputing the Z-score from P for every SNP will not be
 #' perfectly correct and may result in a loss of power. This should only be done
@@ -79,20 +79,20 @@
 #' @param convert_n_int Binary, if N (the number of samples) is not an integer,
 #' should this be rounded? Default is TRUE.
 #' @param impute_beta Binary, whether BETA should be imputed using other effect
-#' data if it isn't present in the sumstats. Note that this imputation is an 
-#' approximation (for Z & SE approach) so could have an effect on downstream 
-#' analysis. Use with caution. The different methods MungeSumstats will try and 
-#' impute beta (in this order or priority) are: 
+#' data if it isn't present in the sumstats. Note that this imputation is an
+#' approximation (for Z & SE approach) so could have an effect on downstream
+#' analysis. Use with caution. The different methods MungeSumstats will try and
+#' impute beta (in this order or priority) are:
 #' 1. log(OR)  2. Z x SE
 #' Default value is FALSE.
 #' @param es_is_beta Binary, whether to map ES to BETA. We take BETA to be any
 #' BETA-like value (including Effect Size). If this is not the case for your
 #' sumstats, change this to FALSE. Default is TRUE.
-#' @param impute_se Binary, whether the standard error should be imputed using 
-#' other effect data if it isn't present in the sumstats. Note that this 
-#' imputation is an approximation so could have an effect on downstream 
+#' @param impute_se Binary, whether the standard error should be imputed using
+#' other effect data if it isn't present in the sumstats. Note that this
+#' imputation is an approximation so could have an effect on downstream
 #' analysis. Use with caution. The different methods MungeSumstats will try and
-#' impute se (in this order or priority) are: 
+#' impute se (in this order or priority) are:
 #' 1. BETA / Z  2. abs(BETA/ qnorm(P/2))
 #' Default is FALSE.
 #' @param analysis_trait If multiple traits were studied, name of the trait for
@@ -114,11 +114,14 @@
 #' @param N_std numeric The number of standard deviations above the mean a SNP's
 #' N is needed to be removed. Default is 5.
 #' @param N_dropNA Drop rows where N is missing.Default is TRUE.
-#' @param rmv_chr vector or character The chromosomes on which the SNPs should
-#' be removed. Use NULL if no filtering necessary. Default is X, Y and
-#' mitochondrial.
-#' @param rmv_chrPrefix Remove "chr" or "CHR" from chromosome names. Default is
-#' TRUE.
+#' @param chr_style Chromosome naming style to use in the formatted summary
+#'   statistics file ("NCBI", "UCSC", "dbSNP", or "Ensembl"). The NCBI and
+#'   Ensembl styles both code chromosomes as `1-22, X, Y, MT`; the UCSC style is
+#'   `chr1-chr22, chrX, chrY, chrM`; and the dbSNP style is
+#'   `ch1-ch22, chX, chY, chMT`. Default is Ensembl.
+#' @param rmv_chr Chromosomes to exclude from the formatted summary statistics
+#'   file. Use NULL if no filtering is necessary. Default is `c("X", "Y", "MT")`
+#'   which removes all non-autosomal SNPs.
 #' @param on_ref_genome Binary Should a check take place that all SNPs are on
 #' the reference genome by SNP ID. Default is TRUE.
 #' @param strand_ambig_filter Binary Should SNPs with strand-ambiguous alleles
@@ -150,15 +153,15 @@
 #' FRQ column should be renamed to MAJOR_ALLELE_FRQ if the frequency values
 #' appear to relate to the major allele i.e. >0.5. By default this mapping won't
 #' occur i.e. is TRUE.
-#' @param indels Binary does your Sumstats file contain Indels? These don't 
-#' exist in our reference file so they will be excluded from checks if this 
+#' @param indels Binary does your Sumstats file contain Indels? These don't
+#' exist in our reference file so they will be excluded from checks if this
 #' value is TRUE. Default is TRUE.
-#' @param drop_indels Binary, should any indels found in the sumstats be 
-#' dropped? These can not be checked against a reference dataset and will have 
-#' the same RS ID and position as SNPs which can affect downstream analysis. 
+#' @param drop_indels Binary, should any indels found in the sumstats be
+#' dropped? These can not be checked against a reference dataset and will have
+#' the same RS ID and position as SNPs which can affect downstream analysis.
 #' Default is False.
 #' @param dbSNP version of dbSNP to be used for imputation (144 or 155).
-#' @param check_dups whether to check for duplicates - if formatting QTL 
+#' @param check_dups whether to check for duplicates - if formatting QTL
 #' datasets this should be set to FALSE otherwise keep as TRUE. Default is TRUE.
 #' @param sort_coordinates Whether to sort by coordinates of resulting sumstats
 #' @param nThread Number of threads to use for parallel processes.
@@ -173,8 +176,8 @@
 #' @param return_format If return_data is TRUE. Object type to be returned
 #' ("data.table","vranges","granges").
 #' @param ldsc_format DEPRECATED, do not use. Use save_format="LDSC" instead.
-#' @param save_format Output format of sumstats. Options are NULL - standardised 
-#' output format from MungeSumstats, LDSC - output format compatible with LDSC 
+#' @param save_format Output format of sumstats. Options are NULL - standardised
+#' output format from MungeSumstats, LDSC - output format compatible with LDSC
 #' and openGWAS - output compatible with openGWAS VCFs. Default is NULL.
 #' @param log_folder_ind Binary Should log files be stored containing all
 #' filtered out SNPs (separate file per filter). The data is outputted in the
@@ -184,10 +187,10 @@
 #' @param log_mungesumstats_msgs Binary Should a log be stored containing all
 #' messages and errors printed by MungeSumstats in a run. Default is FALSE
 #' @param log_folder Filepath to the directory for the log files and the log of
-#' MungeSumstats messages to be stored. Default is a temporary directory. Note 
-#' the name of the log files (log messages and log outputs) are now the same as 
-#' the name of the file specified in the save path parameter with the extension 
-#' '_log_msg.txt' and '_log_output.txt' respectively.  
+#' MungeSumstats messages to be stored. Default is a temporary directory. Note
+#' the name of the log files (log messages and log outputs) are now the same as
+#' the name of the file specified in the save path parameter with the extension
+#' '_log_msg.txt' and '_log_output.txt' respectively.
 #' @param imputation_ind Binary Should a column be added for each imputation
 #' step to show what SNPs have imputed values for differing fields. This
 #' includes a field denoting SNP allele flipping (flipped). On the flipped
@@ -223,7 +226,7 @@ format_sumstats <- function(path,
                             force_new_z = FALSE,
                             compute_n = 0L,
                             convert_n_int = TRUE,
-                            impute_beta = FALSE, 
+                            impute_beta = FALSE,
                             es_is_beta = TRUE,
                             impute_se = FALSE,
                             analysis_trait = NULL,
@@ -234,8 +237,8 @@ format_sumstats <- function(path,
                             effect_columns_nonzero = FALSE,
                             N_std = 5,
                             N_dropNA = TRUE,
+                            chr_style = "Ensembl",
                             rmv_chr = c("X", "Y", "MT"),
-                            rmv_chrPrefix = TRUE,
                             on_ref_genome = TRUE,
                             strand_ambig_filter = FALSE,
                             allele_flip_check = TRUE,
@@ -272,7 +275,7 @@ format_sumstats <- function(path,
     orig_dims <- NULL
     log_files <- vector(mode = "list")
     t1 <- Sys.time()
-    
+
     #### Check 1: Ensure save_path is correct.   ####
     check_save_out <- check_save_path(
         save_path = save_path,
@@ -288,7 +291,7 @@ format_sumstats <- function(path,
         )
         sort_coordinates <- TRUE
     }
-    
+
     #### Recognize previously formatted files ####
     if (file.exists(check_save_out$save_path) && (force_new == FALSE)) {
         message(
@@ -300,7 +303,7 @@ format_sumstats <- function(path,
         # Avoid reloading ref genome every time,
         # save it to this parent environment
         # after being made once - speed up code
-        
+
         # Check input parameters
         validate_parameters(
             path = path,
@@ -318,6 +321,7 @@ format_sumstats <- function(path,
             effect_columns_nonzero = effect_columns_nonzero,
             N_std = N_std,
             N_dropNA = N_dropNA,
+            chr_style = chr_style,
             rmv_chr = rmv_chr,
             on_ref_genome = on_ref_genome,
             strand_ambig_filter = strand_ambig_filter,
@@ -344,7 +348,7 @@ format_sumstats <- function(path,
             tabix_index = tabix_index,
             chain_source = chain_source
         )
-        
+
         # save messages to file if user specified
         if (log_mungesumstats_msgs) {
             #get name of file from save_path
@@ -388,11 +392,11 @@ format_sumstats <- function(path,
         # from different studies are differently formatted),
         # so it makes more sense to just make a
         # temporary file <tmp>, and return the address of the temp
-        
+
         #Ensure dbSNP is a integer (make using it later easier)
         #already validated in validate param function
         dbSNP <- as.integer(dbSNP)
-        
+
         ####  Check 2: Check input format and import ####
         sumstats_return <- list()
         # if data.frame/data.table read it in directly, otherwise read from path
@@ -407,12 +411,12 @@ format_sumstats <- function(path,
                 nThread = nThread
             )
         }
-        
+
         #If es_is_beta remove from mapping file if present
-        if (!es_is_beta & nrow(mapping_file[mapping_file$Uncorrected=="ES" & 
+        if (!es_is_beta & nrow(mapping_file[mapping_file$Uncorrected=="ES" &
                                            mapping_file$Corrected=="BETA",])>=1)
           {
-          mapping_file <- mapping_file[!(mapping_file$Uncorrected=="ES" & 
+          mapping_file <- mapping_file[!(mapping_file$Uncorrected=="ES" &
                                          mapping_file$Corrected=="BETA"),]
           #Add ES mapping
           es_cols <- data.frame("Uncorrected"=c("ES","EFFECT_SIZE",
@@ -426,14 +430,14 @@ format_sumstats <- function(path,
                                 "Corrected"=rep("ES",14))
           mapping_file <- rbind(mapping_file,es_cols)
         }
-        
+
         #### Check 3:Standardise headers for all OS ####
         sumstats_return <-
             standardise_sumstats_column_headers_crossplatform(
                 sumstats_dt = sumstats_return$sumstats_dt,
                 mapping_file = mapping_file
             )
-        
+
         #### If save_format=LDSC, make sure all arguments comply with with.
         check_ldsc <- check_ldsc_format(
             sumstats_dt = sumstats_return$sumstats_dt,
@@ -446,12 +450,12 @@ format_sumstats <- function(path,
         convert_n_int <- check_ldsc$convert_n_int
         allele_flip_check <- check_ldsc$allele_flip_check
         compute_z <- check_ldsc$compute_z
-        
+
         ### Report the number of SNP/CHR/etc. before any filtering
         ### (but after header formatting)
         report_summary(sumstats_dt = sumstats_return$sumstats_dt)
         orig_dims <- dim(sumstats_return$sumstats_dt)
-        
+
         #### Check 4: Check if multi models used
         # or multi traits tested in GWAS ####
         sumstats_return <-
@@ -462,7 +466,7 @@ format_sumstats <- function(path,
                 ignore_multi_trait = ignore_multi_trait,
                 mapping_file = mapping_file
             )
-        
+
         #### Check 33: Check if multi RS ID SNPs in one line ####
         sumstats_return <-
             check_multi_rs_snp(
@@ -478,10 +482,10 @@ format_sumstats <- function(path,
             )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #before running inference of genome build, do any formatting
         #not using the reference sets
-        
+
         #### Infer reference genome if necessary ####
         if (is.null(ref_genome)) {
             ref_genome <- get_genome_build(
@@ -492,7 +496,7 @@ format_sumstats <- function(path,
                 dbSNP=dbSNP
             )
         }
-        
+
         #### Check 5: Check for uniformity in SNP col - ####
         #### no mix of rs/missing rs/chr:bp ####
         sumstats_return <-
@@ -519,16 +523,16 @@ format_sumstats <- function(path,
                 path = path
             )
         col_headers <- names(sumstats_return$sumstats_dt)
-        
+
         #Ensure A1 and A2 are upper case
         sumstats_return <-
             make_allele_upper(sumstats_dt = sumstats_return$sumstats_dt,
                               log_files = log_files)
         # update values
         log_files <- sumstats_return$log_files
-        
+
         # Series of checks if CHR or BP columns aren't present
-        if (sum(c("CHR", "BP") %in% col_headers) != 2) { 
+        if (sum(c("CHR", "BP") %in% col_headers) != 2) {
             msg <-
                 paste0(
                     "Summary statistics file does not have",
@@ -536,14 +540,14 @@ format_sumstats <- function(path,
                     "Checking to see if they are joined in another column."
                 )
             message(msg)
-            
+
             #### Check 6: check if CHR:BP:A2:A1 merged to 1 column
             sumstats_return <- check_four_step_col(
                 sumstats_dt =
                     sumstats_return$sumstats_dt,
                 path = path
             )
-            
+
             #### Check 7: check if there is a column of
             # data with CHR:BP format ####
             sumstats_return <- check_two_step_col(
@@ -559,7 +563,7 @@ format_sumstats <- function(path,
                     mapping_file = mapping_file
                 )
         }
-        
+
         #### Check 38: validate BP
         sumstats_return <- check_bp_range(
           sumstats_dt = sumstats_return$sumstats_dt,
@@ -574,7 +578,7 @@ format_sumstats <- function(path,
         )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 8: check if CHR and BP are missing but SNP is present ####
         sumstats_return <-
             check_no_chr_bp(
@@ -611,7 +615,7 @@ format_sumstats <- function(path,
         )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 25: check that all snps are present on reference genome ####
         sumstats_return <- check_on_ref_genome(
             sumstats_dt =
@@ -633,7 +637,7 @@ format_sumstats <- function(path,
         log_files <- sumstats_return$log_files
         rsids <- sumstats_return$rsids # update rsids
         sumstats_return$rsids <- NULL
-        
+
         #### Check 10: check if SNP is present but A1 and/or A2 is missing ####
         sumstats_return <-
             check_no_allele(
@@ -656,17 +660,17 @@ format_sumstats <- function(path,
         sumstats_return$rsids <- NULL
         # get updated flip
         allele_flip_check <- sumstats_return$allele_flip_check
-        
+
         #### Check 11: check that all the vital columns are present ###
         check_vital_col(sumstats_dt = sumstats_return$sumstats_dt)
-        
+
         #### Check 12: check there is at least one signed sumstats column ###
-        sumstats_return <- 
+        sumstats_return <-
             check_signed_col(
-                sumstats_dt = sumstats_return$sumstats_dt, 
+                sumstats_dt = sumstats_return$sumstats_dt,
                 impute_beta = impute_beta,
                 log_folder_ind = log_folder_ind,
-                rsids = rsids, 
+                rsids = rsids,
                 imputation_ind = imputation_ind,
                 check_save_out = check_save_out,
                 tabix_index = tabix_index,
@@ -677,7 +681,7 @@ format_sumstats <- function(path,
         log_files <- sumstats_return$log_files
         rsids <- sumstats_return$rsids # update rsids
         sumstats_return$rsids <- NULL
-        
+
         #### Check 13: check for allele flipping ####
         sumstats_return <-
             check_allele_flip(
@@ -703,7 +707,7 @@ format_sumstats <- function(path,
         log_files <- sumstats_return$log_files
         rsids <- sumstats_return$rsids # update rsids
         sumstats_return$rsids <- NULL
-        
+
         #### Check 14: check first three column headers are SNP, CHR, BP ###
         ### (in that order) and also check A1 and A2 are fourth and fifth####
         sumstats_return <-
@@ -711,7 +715,7 @@ format_sumstats <- function(path,
                 sumstats_dt = sumstats_return$sumstats_dt,
                 path = path
             )
-        
+
         #### Check 15: Keep only rows which have the number
         # of columns expected ####
         sumstats_return <-
@@ -726,7 +730,7 @@ format_sumstats <- function(path,
             )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 16: check for duplicated columns ####
         # The formatting process can (rarely) result in duplicated columns,
         # i.e. CHR, if CHR:BP is expanded and
@@ -735,7 +739,7 @@ format_sumstats <- function(path,
             sumstats_dt = sumstats_return$sumstats_dt,
             path = path
         )
-        
+
         #### Check 17: check for small P-values (<=5e-324) ####
         sumstats_return <-
             check_small_p_val(
@@ -743,16 +747,16 @@ format_sumstats <- function(path,
                 convert_small_p = convert_small_p,
                 imputation_ind = imputation_ind
             )
-        
+
         #### Check 17.5: check for large (>1) and neg (<0)  p-values ####
         sumstats_return <-
             check_range_p_val(
                 sumstats_dt = sumstats_return$sumstats_dt,
-                convert_large_p = convert_large_p, 
+                convert_large_p = convert_large_p,
                 convert_neg_p = convert_neg_p,
                 imputation_ind = imputation_ind
             )
-        
+
         #### Check 18: check is N column not all integers,
         # if so round it up ####
         sumstats_return <-
@@ -762,7 +766,7 @@ format_sumstats <- function(path,
                 convert_n_int = convert_n_int,
                 imputation_ind = imputation_ind
             )
-        
+
         #### Check 19: check all rows have SNPs starting with SNP or rs, ####
         #### drop those that don't ####.
         sumstats_return <- check_row_snp(
@@ -776,7 +780,7 @@ format_sumstats <- function(path,
         )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         ### Check 37: Drop Indels ###
         sumstats_return <- check_drop_indels(
           sumstats_dt = sumstats_return$sumstats_dt,
@@ -787,10 +791,10 @@ format_sumstats <- function(path,
           tabix_index = tabix_index,
           nThread = nThread,
           log_files = log_files)
-        
+
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 20: check all rows for duplicated SNPs,
         # remove any that are ####
         sumstats_return <- check_dup_snp(
@@ -824,11 +828,11 @@ format_sumstats <- function(path,
         )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 22: check for low INFO scores ####
         sumstats_return <-
             check_info_score(
-                sumstats_dt = sumstats_return$sumstats_dt, 
+                sumstats_dt = sumstats_return$sumstats_dt,
                 INFO_filter = INFO_filter,
                 log_folder_ind = log_folder_ind,
                 check_save_out = check_save_out,
@@ -838,7 +842,7 @@ format_sumstats <- function(path,
             )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 35: check for low FRQ scores ####
         sumstats_return <-
             check_frq(
@@ -853,7 +857,7 @@ format_sumstats <- function(path,
             )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 30: check standard error is positive ####
         sumstats_return <-
             check_pos_se(
@@ -870,7 +874,7 @@ format_sumstats <- function(path,
             )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 31: check effect columns are not 0 ####
         sumstats_return <-
             check_effect_columns_nonzero(
@@ -885,7 +889,7 @@ format_sumstats <- function(path,
             )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 23: check for N > X std dev above mean ####
         sumstats_return <- check_n_num(
             sumstats_dt = sumstats_return$sumstats_dt,
@@ -900,22 +904,20 @@ format_sumstats <- function(path,
         )
         # update values
         log_files <- sumstats_return$log_files
-        
-        #### Check 24: check that no snps are on specific chromosomes ####
+
+        #### Check 24: standardize the CHR column ####
         sumstats_return <- check_chr(
-            sumstats_dt = sumstats_return$sumstats_dt,
-            path = path,
-            rmv_chr = rmv_chr,
-            rmv_chrPrefix = rmv_chrPrefix,
-            log_folder_ind = log_folder_ind,
-            check_save_out = check_save_out,
-            tabix_index = tabix_index,
-            nThread = nThread,
-            log_files = log_files
+          sumstats_dt = sumstats_return$sumstats_dt,
+          log_files = log_files,
+          check_save_out = check_save_out,
+          rmv_chr = rmv_chr,
+          nThread = nThread,
+          tabix_index = tabix_index,
+          log_folder_ind = log_folder_ind
         )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 26: check that all snps are not strand ambiguous ####
         sumstats_return <- check_strand_ambiguous(
             sumstats_dt =
@@ -932,7 +934,7 @@ format_sumstats <- function(path,
         )
         # update values
         log_files <- sumstats_return$log_files
-        
+
         #### Check 27: check for non-biallelic SNPS ####
         sumstats_return <- check_bi_allelic(
             sumstats_dt =
@@ -952,7 +954,7 @@ format_sumstats <- function(path,
         log_files <- sumstats_return$log_files
         rsids <- sumstats_return$rsids # update rsids
         sumstats_return$rsids <- NULL
-        
+
         #### Check 28: Compute Z-score ####
         sumstats_return <- check_zscore(
             sumstats_dt =
@@ -962,7 +964,7 @@ format_sumstats <- function(path,
             imputation_ind = imputation_ind,
             mapping_file = mapping_file
         )
-        
+
         #### Check 32: Compute N ####
         sumstats_return <- compute_nsize(
             sumstats_dt =
@@ -970,15 +972,15 @@ format_sumstats <- function(path,
             compute_n = compute_n,
             imputation_ind = imputation_ind
         )
-        
+
         #### Check 36: Ensure FRQ is MAF ####
         sumstats_return$sumstats_dt <- check_frq_maf(
             sumstats_dt =
                 sumstats_return$sumstats_dt,
             frq_is_maf = frq_is_maf
         )
-        
-        
+
+
         #### Check 34: Perform liftover ####
         sumstats_return$sumstats_dt <- liftover(
             sumstats_dt =
@@ -991,7 +993,7 @@ format_sumstats <- function(path,
         #update ref genome of data
         if(!is.null(convert_ref_genome))
           ref_genome <- convert_ref_genome
-        
+
         #### Check 29: Sort rows by genomic coordinates ####
         sumstats_return$sumstats_dt <- sort_coords(
             sumstats_dt =
@@ -999,7 +1001,11 @@ format_sumstats <- function(path,
             sort_coordinates =
                 sort_coordinates
         )
-        
+
+        ### Check 39: Ensure CHR follows the requested style ###
+        CHR <- NULL
+        sumstats_return$sumstats_dt[, CHR := GenomeInfoDb::mapSeqlevels(CHR, style = chr_style)]
+
         #### WRITE data.table TO PATH ####
         check_save_out$save_path <- write_sumstats(
             sumstats_dt = sumstats_return$sumstats_dt,
@@ -1013,7 +1019,7 @@ format_sumstats <- function(path,
             return_path = TRUE
         )
         rm(rsids) # free up memory
-        
+
         #### Report summary ####
         report_summary(
             sumstats_dt = sumstats_return$sumstats_dt,
@@ -1025,20 +1031,20 @@ format_sumstats <- function(path,
     message(
         "Done munging in ",
         round(difftime(t2, t1, units = "mins"), 3), " minutes."
-    ) 
-    
+    )
+
     #### Preview sumstats ####
     preview_sumstats(
         save_path = check_save_out$save_path,
         nrows = 5L
     )
-    
+
     # if user wanted log of messages remember to unsink at end
     if (log_mungesumstats_msgs) {
         sink(NULL, type = "message")
         sink(NULL, type = "output")
     }
-    
+
     if (return_data) {
         message("Returning data directly.")
         #### Load data into memory when a pre-existing file is being used
@@ -1056,7 +1062,7 @@ format_sumstats <- function(path,
         )
         # if user wants log files return a list
         if (log_folder_ind || log_mungesumstats_msgs) {
-            return(list("sumstats" = out, 
+            return(list("sumstats" = out,
                         "log_files" = log_files))
         }
         return(out)
@@ -1070,4 +1076,4 @@ format_sumstats <- function(path,
         }
         return(check_save_out$save_path) # Returns address of modified file
     }
-}
\ No newline at end of file
+}
diff --git a/R/validate_parameters.R b/R/validate_parameters.R
index ffba115..019e84b 100644
--- a/R/validate_parameters.R
+++ b/R/validate_parameters.R
@@ -18,6 +18,7 @@ validate_parameters <- function(path,
                                 effect_columns_nonzero,
                                 N_std,
                                 N_dropNA,
+                                chr_style,
                                 rmv_chr,
                                 on_ref_genome,
                                 strand_ambig_filter,
@@ -43,7 +44,7 @@ validate_parameters <- function(path,
                                 mapping_file,
                                 tabix_index,
                                 chain_source) {
-    # Checking if the file exists should happen first - 
+    # Checking if the file exists should happen first -
     # can pass dt/df of sumstats
     pth_msg <- paste0(
         "Path to GWAS sumstats is not valid, pass a file path or a ",
@@ -80,7 +81,7 @@ validate_parameters <- function(path,
       "The chosen chain file source to convert to must be one of ",
       "Ensembl or UCSC ('ensembl','ucsc')"
     )
-    if(length(chain_source)>1 || !tolower(chain_source) %in% c("ucsc", 
+    if(length(chain_source)>1 || !tolower(chain_source) %in% c("ucsc",
                                                                "ensembl")){
       stop(chain_msg)
     }
@@ -174,13 +175,13 @@ validate_parameters <- function(path,
           stop(GRCH38_msg2)
         }
         #dbSNP
-        if (as.integer(dbSNP)==144 && 
+        if (as.integer(dbSNP)==144 &&
             !requireNamespace("SNPlocs.Hsapiens.dbSNP144.GRCh37",
             quietly = TRUE
         )) {
             stop(GRCH37_msg1)
         }
-        if (as.integer(dbSNP)==155 && 
+        if (as.integer(dbSNP)==155 &&
             !requireNamespace("SNPlocs.Hsapiens.dbSNP155.GRCh37",
                             quietly = TRUE
         )) {
@@ -265,14 +266,14 @@ validate_parameters <- function(path,
         stop("`ldsc_format` has been deprecated. Use `save_format='LDSC'`.")
     }
     #save_format
-    if(!is.null(save_format) && 
+    if(!is.null(save_format) &&
        !tolower(save_format) %in% c("ldsc","opengwas")){
       stop("save_format must be NULL or one of LDSC or openGWAS")
     }
     opengws_err <- paste0("IEU OpenGWAS format only available when saving as ",
                           "VCF. Set `write_vcf=True` and rerun ",
                           "`format_sumstats()`")
-    if(!is.null(save_format) && 
+    if(!is.null(save_format) &&
         tolower(save_format)=="opengwas" & isFALSE(write_vcf))
       stop(opengws_err)
     if (!is.logical(pos_se)) {
@@ -281,7 +282,7 @@ validate_parameters <- function(path,
     if (!is.logical(effect_columns_nonzero)) {
         stop("effect_columns_nonzero must be either TRUE or FALSE")
     }
-    if (!is.logical(effect_columns_nonzero)) {
+    if (!is.logical(imputation_ind)) {
         stop("imputation_ind must be either TRUE or FALSE")
     }
     if (!is.logical(log_folder_ind)) {
@@ -308,7 +309,7 @@ validate_parameters <- function(path,
                               "passing to MungeSumstats.")
       stop(compute_n_msg)
     }
-    
+
     if (!is.numeric(compute_n) || compute_n < 0) {
         if (is.character(compute_n)) {
             methods <- c("ldsc", "giant", "metal", "sum")
@@ -324,17 +325,20 @@ validate_parameters <- function(path,
             stop("compute_n must be 0 or an integer value")
         }
     }
-    # Check rmv_chr choices all valid chromosomes
+
+    # Check that chr_style is a valid choice
+    styles <- c("NCBI", "UCSC", "dbSNP", "Ensembl")
+    if (!(chr_style %in% styles)) {
+      stop("chr_style must be one of ", paste(styles, collapse = ", "))
+    }
+    # Check that rmv_chr choices are all valid chromosomes
+    # according to the Ensembl/NCBI naming style
     chrs <- c(as.character(seq_len(22)), "X", "Y", "MT")
-    chr_msg <-
-        paste0(
-            "rmv_chr choices must be one/or more of: \n",
-            paste(chrs, collapse = ", ")
-        )
     if (!is.null(rmv_chr)) {
-        if (!all(rmv_chr %in% chrs)) {
-            stop(chr_msg)
-        }
+      if (!all(rmv_chr %in% chrs)) {
+        stop("rmv_chr choices must be one or more of: \n",
+             paste(chrs, collapse = ", "))
+      }
     }
     # check return_format
     rf_msg <- paste0(
@@ -379,9 +383,9 @@ validate_parameters <- function(path,
             mapping_file[, toupper(colnames(mapping_file)) == "CORRECTED"])) {
         stop(mapping_file_msg)
     }
-    
-    if(tabix_index && 
-       any(!requireNamespace("Rsamtools", quietly = TRUE), 
+
+    if(tabix_index &&
+       any(!requireNamespace("Rsamtools", quietly = TRUE),
            !requireNamespace("MatrixGenerics", quietly = TRUE)) ){
         pkgs <- c("Rsamtools","MatrixGenerics")
         missing_pkgs <- pkgs[!pkgs %in% rownames(utils::installed.packages())]
diff --git a/README.Rmd b/README.Rmd
index aa75b26..24a5c07 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -77,20 +77,20 @@ Note that there is also a
 
 Note that for a number of the checks implored by `MungeSumstats` a reference 
 genome is used. If your GWAS summary statistics file of interest relates to
-*GRCh38*, you will need to install `SNPlocs.Hsapiens.dbSNP144.GRCh38` and 
+*GRCh38*, you will need to install `SNPlocs.Hsapiens.dbSNP155.GRCh38` and 
 `BSgenome.Hsapiens.NCBI.GRCh38` from Bioconductor as follows:
 
 ```R
-BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh38")
+BiocManager::install("SNPlocs.Hsapiens.dbSNP155.GRCh38")
 BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38")
 ```
 
 If your GWAS summary statistics file of interest relates to *GRCh37*, you will 
-need to install `SNPlocs.Hsapiens.dbSNP144.GRCh37` and 
+need to install `SNPlocs.Hsapiens.dbSNP155.GRCh37` and 
 `BSgenome.Hsapiens.1000genomes.hs37d5` from Bioconductor as follows:
 
 ```R
-BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh37")
+BiocManager::install("SNPlocs.Hsapiens.dbSNP155.GRCh37")
 BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
 ```
 
@@ -141,5 +141,6 @@ development:
  * [Shea Andrews](https://github.com/sjfandrews)
  * [Jonathan Griffiths](https://github.com/jonathangriffiths)
  * [Kitty Murphy](https://github.com/KittyMurphy)
+ * [Mykhaylo Malakhov](https://github.com/MykMal)
  
 # References
diff --git a/README.md b/README.md
index 89ee350..d95a0d6 100644
--- a/README.md
+++ b/README.md
@@ -2,18 +2,18 @@
 ================
 <h5> ¶ <i>Authors</i>: Alan Murphy, Brian Schilder and Nathan Skene ¶
 </h5>
-<h5> ¶ <i>Updated</i>: Jan-17-2023 ¶ </h5>
+<h5> ¶ <i>Updated</i>: Jul-13-2023 ¶ </h5>
 
 <!-- Readme.md is generated from Readme.Rmd. Please edit that file -->
 <!-- badges: start -->
 
-[![](https://img.shields.io/badge/release%20version-1.6.0-black.svg)](https://www.bioconductor.org/packages/MungeSumstats)
-[![](https://img.shields.io/badge/devel%20version-1.7.14-black.svg)](https://github.com/neurogenomics/MungeSumstats)
+[![](https://img.shields.io/badge/release%20version-1.8.0-black.svg)](https://www.bioconductor.org/packages/MungeSumstats)
+[![](https://img.shields.io/badge/devel%20version-1.9.11-black.svg)](https://github.com/neurogenomics/MungeSumstats)
 [![R build
 status](https://github.com/neurogenomics/MungeSumstats/workflows/rworkflows/badge.svg)](https://github.com/neurogenomics/MungeSumstats/actions)
 [![](https://img.shields.io/github/last-commit/neurogenomics/MungeSumstats.svg)](https://github.com/neurogenomics/MungeSumstats/commits/master)
-[![](https://app.codecov.io/gh/neurogenomics/MungeSumstats/branch/master/graph/badge.svg)](https://app.codecov.io/gh/neurogenomics/MungeSumstats)
-[![](https://img.shields.io/badge/download-2645/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/MungeSumstats)
+[![](https://codecov.io/gh/neurogenomics/MungeSumstats/branch/master/graph/badge.svg)](https://codecov.io/gh/neurogenomics/MungeSumstats)
+[![](https://img.shields.io/badge/download-5460/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/MungeSumstats)
 [![License:
 Artistic-2.0](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0)
 [![](https://img.shields.io/badge/doi-https://doi.org/10.1093/bioinformatics/btab665-blue.svg)](https://doi.org/https://doi.org/10.1093/bioinformatics/btab665)
@@ -70,23 +70,26 @@ You can then load the package and data package:
 library(MungeSumstats)
 ```
 
+Note that there is also a [docker image for
+MungeSumstats](https://hub.docker.com/r/neurogenomicslab/mungesumstats).
+
 Note that for a number of the checks implored by `MungeSumstats` a
 reference genome is used. If your GWAS summary statistics file of
 interest relates to *GRCh38*, you will need to install
-`SNPlocs.Hsapiens.dbSNP144.GRCh38` and `BSgenome.Hsapiens.NCBI.GRCh38`
+`SNPlocs.Hsapiens.dbSNP155.GRCh38` and `BSgenome.Hsapiens.NCBI.GRCh38`
 from Bioconductor as follows:
 
 ``` r
-BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh38")
+BiocManager::install("SNPlocs.Hsapiens.dbSNP155.GRCh38")
 BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38")
 ```
 
 If your GWAS summary statistics file of interest relates to *GRCh37*,
-you will need to install `SNPlocs.Hsapiens.dbSNP144.GRCh37` and
+you will need to install `SNPlocs.Hsapiens.dbSNP155.GRCh37` and
 `BSgenome.Hsapiens.1000genomes.hs37d5` from Bioconductor as follows:
 
 ``` r
-BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh37")
+BiocManager::install("SNPlocs.Hsapiens.dbSNP155.GRCh37")
 BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
 ```
 
@@ -143,6 +146,7 @@ We would like to acknowledge all those who have contributed to
 - [Shea Andrews](https://github.com/sjfandrews)
 - [Jonathan Griffiths](https://github.com/jonathangriffiths)
 - [Kitty Murphy](https://github.com/KittyMurphy)
+- [Mykhaylo Malakhov](https://github.com/MykMal)
 
 # References
 
diff --git a/man/check_chr.Rd b/man/check_chr.Rd
index 949d9c6..07f5a9e 100644
--- a/man/check_chr.Rd
+++ b/man/check_chr.Rd
@@ -2,51 +2,47 @@
 % Please edit documentation in R/check_chr.R
 \name{check_chr}
 \alias{check_chr}
-\title{Ensure all SNPs on specified chromosomes are removed}
+\title{Standardize the CHR column}
 \usage{
 check_chr(
   sumstats_dt,
-  path,
-  rmv_chr,
-  log_folder_ind,
+  log_files,
   check_save_out,
-  tabix_index,
+  rmv_chr,
   nThread,
-  log_files,
-  make_uppercase = TRUE,
-  rmv_chrPrefix = TRUE
+  tabix_index,
+  log_folder_ind
 )
 }
 \arguments{
-\item{path}{Filepath for the summary statistics file to be formatted. A
-dataframe or datatable of the summary statistics file can also be passed
-directly to MungeSumstats using the path parameter.}
+\item{sumstats_dt}{data.table with summary statistics}
 
-\item{rmv_chr}{vector or character The chromosomes on which the SNPs should
-be removed. Use NULL if no filtering necessary. Default is X, Y and
-mitochondrial.}
+\item{log_files}{list of locations for all log files}
 
-\item{log_folder_ind}{Binary Should log files be stored containing all
-filtered out SNPs (separate file per filter). The data is outputted in the
-same format specified for the resulting sumstats file. The only exception to
-this rule is if output is vcf, then log file saved as .tsv.gz. Default is
-FALSE.}
+\item{check_save_out}{list of parameters for saved files}
 
-\item{tabix_index}{Index the formatted summary statistics with
-\href{http://www.htslib.org/doc/tabix.html}{tabix} for fast querying.}
+\item{rmv_chr}{Chromosomes to exclude from the formatted summary statistics
+file. Use NULL if no filtering is necessary. Default is \code{c("X", "Y", "MT")}
+which removes all non-autosomal SNPs.}
 
 \item{nThread}{Number of threads to use for parallel processes.}
 
-\item{log_files}{list of log file locations}
+\item{tabix_index}{Index the formatted summary statistics with
+\href{http://www.htslib.org/doc/tabix.html}{tabix} for fast querying.}
 
-\item{rmv_chrPrefix}{Remove "chr" or "CHR" from chromosome names. Default is
-TRUE.}
+\item{log_folder_ind}{Binary Should log files be stored containing all
+filtered out SNPs (separate file per filter). The data is outputted in the
+same format specified for the resulting sumstats file. The only exception to
+this rule is if output is vcf, then log file saved as .tsv.gz. Default is
+FALSE.}
 }
 \value{
-list containing sumstats_dt, the modified summary statistics data
-table object and the log file list
+list containing the updated summary statistics data.table and the
+updated log file locations list
 }
 \description{
-Ensure all SNPs on specified chromosomes are removed
+Maps chromosome names to the default Ensembl/NCBI naming style and removes
+SNPs with nonstandard CHR entries. Optionally, also removes SNPs on
+user-specified chromosomes.
 }
 \keyword{internal}
diff --git a/man/format_sumstats.Rd b/man/format_sumstats.Rd
index ed104bd..a763c4a 100644
--- a/man/format_sumstats.Rd
+++ b/man/format_sumstats.Rd
@@ -27,8 +27,8 @@ format_sumstats(
   effect_columns_nonzero = FALSE,
   N_std = 5,
   N_dropNA = TRUE,
+  chr_style = "Ensembl",
   rmv_chr = c("X", "Y", "MT"),
-  rmv_chrPrefix = TRUE,
   on_ref_genome = TRUE,
   strand_ambig_filter = FALSE,
   allele_flip_check = TRUE,
@@ -165,12 +165,15 @@ N is needed to be removed. Default is 5.}
 
 \item{N_dropNA}{Drop rows where N is missing.Default is TRUE.}
 
-\item{rmv_chr}{vector or character The chromosomes on which the SNPs should
-be removed. Use NULL if no filtering necessary. Default is X, Y and
-mitochondrial.}
+\item{chr_style}{Chromosome naming style to use in the formatted summary
+statistics file ("NCBI", "UCSC", "dbSNP", or "Ensembl"). The NCBI and
+Ensembl styles both code chromosomes as \verb{1-22, X, Y, MT}; the UCSC style is
+\verb{chr1-chr22, chrX, chrY, chrM}; and the dbSNP style is
+\verb{ch1-ch22, chX, chY, chMT}. Default is Ensembl.}
 
-\item{rmv_chrPrefix}{Remove "chr" or "CHR" from chromosome names. Default is
-TRUE.}
+\item{rmv_chr}{Chromosomes to exclude from the formatted summary statistics
+file. Use NULL if no filtering is necessary. Default is \code{c("X", "Y", "MT")}
+which removes all non-autosomal SNPs.}
 
 \item{on_ref_genome}{Binary Should a check take place that all SNPs are on
 the reference genome by SNP ID. Default is TRUE.}
diff --git a/man/import_sumstats.Rd b/man/import_sumstats.Rd
index 37f45a5..9285bdd 100644
--- a/man/import_sumstats.Rd
+++ b/man/import_sumstats.Rd
@@ -138,11 +138,14 @@ Those that do are removed(if present in sumstats file). Default FALSE.}
     \item{\code{N_std}}{numeric The number of standard deviations above the mean a SNP's
 N is needed to be removed. Default is 5.}
     \item{\code{N_dropNA}}{Drop rows where N is missing.Default is TRUE.}
-    \item{\code{rmv_chr}}{vector or character The chromosomes on which the SNPs should
-be removed. Use NULL if no filtering necessary. Default is X, Y and
-mitochondrial.}
-    \item{\code{rmv_chrPrefix}}{Remove "chr" or "CHR" from chromosome names. Default is
-TRUE.}
+    \item{\code{chr_style}}{Chromosome naming style to use in the formatted summary
+statistics file ("NCBI", "UCSC", "dbSNP", or "Ensembl"). The NCBI and
+Ensembl styles both code chromosomes as \verb{1-22, X, Y, MT}; the UCSC style is
+\verb{chr1-chr22, chrX, chrY, chrM}; and the dbSNP style is
+\verb{ch1-ch22, chX, chY, chMT}. Default is Ensembl.}
+    \item{\code{rmv_chr}}{Chromosomes to exclude from the formatted summary statistics
+file. Use NULL if no filtering is necessary. Default is \code{c("X", "Y", "MT")}
+which removes all non-autosomal SNPs.}
     \item{\code{on_ref_genome}}{Binary Should a check take place that all SNPs are on
 the reference genome by SNP ID. Default is TRUE.}
     \item{\code{strand_ambig_filter}}{Binary Should SNPs with strand-ambiguous alleles
diff --git a/man/to_GRanges.Rd b/man/to_granges.Rd
similarity index 100%
rename from man/to_GRanges.Rd
rename to man/to_granges.Rd
diff --git a/man/to_VRanges.Rd b/man/to_vranges.Rd
similarity index 100%
rename from man/to_VRanges.Rd
rename to man/to_vranges.Rd
diff --git a/man/validate_parameters.Rd b/man/validate_parameters.Rd
index 70ff058..d9cd1c4 100644
--- a/man/validate_parameters.Rd
+++ b/man/validate_parameters.Rd
@@ -20,6 +20,7 @@ validate_parameters(
   effect_columns_nonzero,
   N_std,
   N_dropNA,
+  chr_style,
   rmv_chr,
   on_ref_genome,
   strand_ambig_filter,
@@ -112,9 +113,15 @@ N is needed to be removed. Default is 5.}
 
 \item{N_dropNA}{Drop rows where N is missing.Default is TRUE.}
 
-\item{rmv_chr}{vector or character The chromosomes on which the SNPs should
-be removed. Use NULL if no filtering necessary. Default is X, Y and
-mitochondrial.}
+\item{chr_style}{Chromosome naming style to use in the formatted summary
+statistics file ("NCBI", "UCSC", "dbSNP", or "Ensembl"). The NCBI and
+Ensembl styles both code chromosomes as \verb{1-22, X, Y, MT}; the UCSC style is
+\verb{chr1-chr22, chrX, chrY, chrM}; and the dbSNP style is
+\verb{ch1-ch22, chX, chY, chMT}. Default is Ensembl.}
+
+\item{rmv_chr}{Chromosomes to exclude from the formatted summary statistics
+file. Use NULL if no filtering is necessary. Default is \code{c("X", "Y", "MT")}
+which removes all non-autosomal SNPs.}
 
 \item{on_ref_genome}{Binary Should a check take place that all SNPs are on
 the reference genome by SNP ID. Default is TRUE.}
diff --git a/tests/testthat/test-multi_traits.R b/tests/testthat/test-multi_traits.R
index 0a2f645..42ed328 100644
--- a/tests/testthat/test-multi_traits.R
+++ b/tests/testthat/test-multi_traits.R
@@ -24,7 +24,7 @@ test_that("Multi-trait GWAS handled correctly", {
             bi_allelic_filter = FALSE,
             allele_flip_check = FALSE,
             sort_coordinates = FALSE,
-            rmv_chrPrefix = FALSE,
+            chr_style = "UCSC",
             dbSNP=144
         )
         reformatted_res <- readLines(reformatted)
@@ -37,7 +37,7 @@ test_that("Multi-trait GWAS handled correctly", {
             "rs1000075\tchr1\t94939420\tC\tT\t94939420\t0.3583\t38959\t-0.0013\t0.0082\t0.8687\t147567\t-0.0043\t0.0044\t0.3259"
         )
         expect_equal(setequal(multi_trait_res_smk, reformatted_res), TRUE)
-    }    
+    }
     else{
         expect_equal(is_32bit_windows, TRUE)
     }
diff --git a/vignettes/MungeSumstats.Rmd b/vignettes/MungeSumstats.Rmd
index 1015542..873b42c 100644
--- a/vignettes/MungeSumstats.Rmd
+++ b/vignettes/MungeSumstats.Rmd
@@ -129,7 +129,8 @@ Tests run by *MungeSumstats* include:
 -   Check for strand-ambiguous SNPs
 -   Check for non-biallelic SNPs (infer from reference genome)
 -   Check for allele flipping
--   Check for SNPs on chromosome X, Y, and mitochondrial SNPs (MT)
+-   Check for SNPs with nonstandard chromosome names
+-   Check for SNPs on excluded chromosomes (removes non-autosomal SNPs by default)
 -   Check for z-score (Z) and impute if missing
 -   Check for N and impute if missing
 -   Check output format is LDSC ready
@@ -339,12 +340,14 @@ conducted by *MungeSumstats* are:
     controls whether the SNPs with a missing N value are dropped or not
     (Default is TRUE).
 -   **N_dropNA** Drop rows where N is missing.Default is TRUE.
--   **rmv_chr** vector or character The chromosomes on which the SNPs
-    should be removed. Use NULL if no filtering necessary. Default is X,
-    Y and mitochondrial.**rmv_chrPrefix** controls whether "chr"/"CHR"
-    is removed from chromosome names (Default is TRUE).
--   **rmv_chrPrefix** Remove "chr" or "CHR" from chromosome names.
-    Default is TRUE.
+-   **chr_style** Chromosome naming style to use in the formatted summary
+    statistics file ("NCBI", "UCSC", "dbSNP", or "Ensembl"). The NCBI and
+    Ensembl styles both code chromosomes as `1-22, X, Y, MT`; the UCSC
+    style is `chr1-chr22, chrX, chrY, chrM`; and the dbSNP style is
+    `ch1-ch22, chX, chY, chMT`. Default is Ensembl.
+-   **rmv_chr** Chromosomes to exclude from the formatted summary
+    statistics file. Use NULL if no filtering is necessary. Default is
+    `c("X", "Y", "MT")` which removes all non-autosomal SNPs.
 -   **on_ref_genome** Binary, should a check take place that all SNPs
     are on the reference genome by SNP ID. Any SNPs not on the reference
     genome, will be corrected from the reference genome (if possible)
@@ -551,7 +554,8 @@ below:
     BETA=0.
 -   **n_large** - SNPs N is N standard deviations greater than the mean.
 -   **n_null** - SNPs N is null.
--   **chr_excl** - SNP is on a chromosome specified to be excluded.
+-   **chr_excl** - SNP has an unrecognized chromosome name or is on a
+    chromosome that was specified to be excluded.
 -   **snp_strand_ambiguous** - SNP is strand ambiguous.
 -   **snp_bi_allelic** - SNP is not bi-allelic.
 -   **MungeSumstats_log_msg** - Text file of all messages to the console