diff --git a/.gitignore b/.gitignore
index 6a6b6d8..6959d3c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
 .Rproj.user
+.Rhistory
 .radian_history
 Scratch.RConsole
-
 /.quarto/
 README.html
 docs
diff --git a/NAMESPACE b/NAMESPACE
index 0454c17..8913399 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,6 +8,7 @@ export(appmamba_rc)
 export(arg)
 export(arg0)
 export(bcftools)
+export(bedtools)
 export(bowtie2)
 export(cellranger)
 export(cmd_background)
diff --git a/R/cmd-bedtools.R b/R/cmd-bedtools.R
new file mode 100644
index 0000000..d6ba1bd
--- /dev/null
+++ b/R/cmd-bedtools.R
@@ -0,0 +1,38 @@
+#' Run bedtools
+#'
+#' The `bedtools` is a powerful toolset for genome arithmetic.
+#' @param subcmd Sub-Command of bedtools. Details see: `r rd_help("bedtools")`.
+#' @param ... `r rd_dots("bedtools")`.
+#' @param bedtools `r rd_cmd("bedtools")`.
+#' @seealso
+#' - <http://bedtools.readthedocs.io/>
+#' - <https://github.com/arq5x/bedtools2/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+bedtools <- make_command(
+  "bedtools",
+  function(subcmd = NULL, ..., bedtools = NULL) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(bedtools, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools$new(cmd = bedtools, ..., subcmd = subcmd)
+  }
+)
+
+BEDTools <- R6Class(
+  "BEDTools",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools",
+    setup_help_params = function() "--help",
+    combine_params = function(subcmd) {
+      if (private$help) {
+        c(super$combine_params(), subcmd)
+      } else {
+        c(subcmd, super$combine_params())
+      }
+    }
+  )
+)
diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
index 1db2bc0..cfa696b 100644
--- a/man/allele_counter.Rd
+++ b/man/allele_counter.Rd
@@ -44,6 +44,7 @@ between some other projects, specifically \code{AscatNGS} and \code{Battenberg}.
 
 Other \code{commands}:
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/bcftools.Rd b/man/bcftools.Rd
index a6960cb..f884a5e 100644
--- a/man/bcftools.Rd
+++ b/man/bcftools.Rd
@@ -34,6 +34,7 @@ All commands work transparently with both VCFs and BCFs, both uncompressed and B
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/bedtools.Rd b/man/bedtools.Rd
new file mode 100644
index 0000000..869b61c
--- /dev/null
+++ b/man/bedtools.Rd
@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cmd-bedtools.R
+\name{bedtools}
+\alias{bedtools}
+\title{Run bedtools}
+\usage{
+bedtools(subcmd = NULL, ..., bedtools = NULL)
+}
+\arguments{
+\item{subcmd}{Sub-Command of bedtools. Details see: \code{cmd_help(bedtools())}.}
+
+\item{...}{<\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \code{bedtools} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \code{cmd_help(bedtools())}.}
+
+\item{bedtools}{A string of path to \code{bedtools} command.}
+}
+\value{
+A \code{command} object.
+}
+\description{
+The \code{bedtools} is a powerful toolset for genome arithmetic.
+}
+\seealso{
+\itemize{
+\item \url{http://bedtools.readthedocs.io/}
+\item \url{https://github.com/arq5x/bedtools2/}
+\item \code{\link[=cmd_wd]{cmd_wd()}}/\code{\link[=cmd_envvar]{cmd_envvar()}}/\code{\link[=cmd_envpath]{cmd_envpath()}}/\code{\link[=cmd_condaenv]{cmd_condaenv()}}
+\item \code{\link[=cmd_on_start]{cmd_on_start()}}/\code{\link[=cmd_on_exit]{cmd_on_exit()}}
+\item \code{\link[=cmd_on_succeed]{cmd_on_succeed()}}/\code{\link[=cmd_on_fail]{cmd_on_fail()}}
+\item \code{\link[=cmd_parallel]{cmd_parallel()}}
+}
+
+Other \code{commands}:
+\code{\link{allele_counter}()},
+\code{\link{bcftools}()},
+\code{\link{bowtie2}()},
+\code{\link{cellranger}()},
+\code{\link{conda}()},
+\code{\link{fastp}()},
+\code{\link{fastq_pair}()},
+\code{\link{gistic2}()},
+\code{\link{kraken2}()},
+\code{\link{kraken_tools}()},
+\code{\link{perl}()},
+\code{\link{pyscenic}()},
+\code{\link{python}()},
+\code{\link{samtools}()},
+\code{\link{seqkit}()},
+\code{\link{snpEff}()},
+\code{\link{trust4}()},
+\code{\link{varscan}()}
+}
+\concept{command}
diff --git a/man/blit-package.Rd b/man/blit-package.Rd
index 8b14d4f..2cdff85 100644
--- a/man/blit-package.Rd
+++ b/man/blit-package.Rd
@@ -14,6 +14,7 @@ An all-encompassing R toolkit designed to streamline the process of calling vari
 Useful links:
 \itemize{
   \item \url{https://github.com/WangLabCSU/blit}
+  \item \url{https://wanglabcsu.github.io/blit/}
   \item Report bugs at \url{https://github.com/WangLabCSU/blit/issues}
 }
 
diff --git a/man/bowtie2.Rd b/man/bowtie2.Rd
index ebafeeb..361c175 100644
--- a/man/bowtie2.Rd
+++ b/man/bowtie2.Rd
@@ -41,6 +41,7 @@ Bowtie 2 supports gapped, local, and paired-end alignment modes.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
index 7ebe5c7..f52c025 100644
--- a/man/cellranger.Rd
+++ b/man/cellranger.Rd
@@ -49,6 +49,7 @@ cellranger(
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/conda.Rd b/man/conda.Rd
index 27fd8b3..9fe0555 100644
--- a/man/conda.Rd
+++ b/man/conda.Rd
@@ -30,6 +30,7 @@ Run conda
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{fastp}()},
diff --git a/man/exec.Rd b/man/exec.Rd
index 552db59..31fb607 100644
--- a/man/exec.Rd
+++ b/man/exec.Rd
@@ -22,6 +22,7 @@ Invoke a System Command
 \itemize{
 \item \code{\link[=allele_counter]{allele_counter()}}
 \item \code{\link[=bcftools]{bcftools()}}
+\item \code{\link[=bedtools]{bedtools()}}
 \item \code{\link[=bowtie2]{bowtie2()}}
 \item \code{\link[=cellranger]{cellranger()}}
 \item \code{\link[=conda]{conda()}}
diff --git a/man/fastp.Rd b/man/fastp.Rd
index 2b023e1..ec3e879 100644
--- a/man/fastp.Rd
+++ b/man/fastp.Rd
@@ -34,6 +34,7 @@ and quality control for FastQ data.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
index b541517..3764bc6 100644
--- a/man/fastq_pair.Rd
+++ b/man/fastq_pair.Rd
@@ -55,6 +55,7 @@ they demand paired end files have the same number of reads.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
index c0196c9..42e9a6a 100644
--- a/man/gistic2.Rd
+++ b/man/gistic2.Rd
@@ -52,6 +52,7 @@ deletion, and it lists genes found in each "wide peak" region.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
index 7bd384f..0a1adc0 100644
--- a/man/kraken2.Rd
+++ b/man/kraken2.Rd
@@ -58,6 +58,7 @@ given k-mer.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
index 8f45d24..fece02b 100644
--- a/man/kraken_tools.Rd
+++ b/man/kraken_tools.Rd
@@ -34,6 +34,7 @@ analysis of Kraken results.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/perl.Rd b/man/perl.Rd
index 8b52cd1..c2b8c8e 100644
--- a/man/perl.Rd
+++ b/man/perl.Rd
@@ -31,6 +31,7 @@ years of development.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
index 63fe252..63f20fc 100644
--- a/man/pyscenic.Rd
+++ b/man/pyscenic.Rd
@@ -31,6 +31,7 @@ Run pyscenic
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/python.Rd b/man/python.Rd
index e8da32b..d4e32a3 100644
--- a/man/python.Rd
+++ b/man/python.Rd
@@ -31,6 +31,7 @@ systems more effectively.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/samtools.Rd b/man/samtools.Rd
index 9364bf7..5b1c133 100644
--- a/man/samtools.Rd
+++ b/man/samtools.Rd
@@ -33,6 +33,7 @@ systems more effectively.
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
index c3b8a54..fcfe722 100644
--- a/man/seqkit.Rd
+++ b/man/seqkit.Rd
@@ -31,6 +31,7 @@ Run seqkit
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/snpEff.Rd b/man/snpEff.Rd
index 192c30b..79b611a 100644
--- a/man/snpEff.Rd
+++ b/man/snpEff.Rd
@@ -33,6 +33,7 @@ It annotates and predicts the effects of genetic variants on genes and proteins
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/trust4.Rd b/man/trust4.Rd
index ea508ac..cdcc7bd 100644
--- a/man/trust4.Rd
+++ b/man/trust4.Rd
@@ -86,6 +86,7 @@ data
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/man/varscan.Rd b/man/varscan.Rd
index edbe779..03ae011 100644
--- a/man/varscan.Rd
+++ b/man/varscan.Rd
@@ -33,6 +33,7 @@ developed at the Genome Institute at Washington University to detect variants in
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
diff --git a/tests/testthat/test-exec.R b/tests/testthat/test-exec.R
index 96557e5..2e848cc 100644
--- a/tests/testthat/test-exec.R
+++ b/tests/testthat/test-exec.R
@@ -3,6 +3,11 @@ testthat::test_that("`allele_counter()` works as expected", {
     allele_counter() |> cmd_help()
 })
 
+testthat::test_that("`bedtools()` works as expected", {
+    testthat::skip_if_not(nzchar(Sys.which("bedtools")))
+    bedtools() |> cmd_help()
+})
+
 testthat::test_that("`cellranger()` works as expected", {
     testthat::skip_if_not(nzchar(Sys.which("cellranger")))
     cellranger() |> cmd_help()