diff --git a/NAMESPACE b/NAMESPACE
index 9866790..d0e26d0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -37,6 +37,7 @@ export(pyscenic)
 export(python)
 export(samtools)
 export(seqkit)
+export(snpEff)
 export(trust4)
 export(trust4_gene_names)
 export(trust4_imgt_annot)
diff --git a/R/cmd-snpEff.R b/R/cmd-snpEff.R
new file mode 100644
index 0000000..e52bc25
--- /dev/null
+++ b/R/cmd-snpEff.R
@@ -0,0 +1,37 @@
+#' Genetic variant annotation, and functional effect prediction toolbox. 
+#' It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
+#'
+#' @param subcmd Sub-Command of snpEff. Details see: `r rd_help("snpEff")`.
+#' @param ... `r rd_dots("snpEff")`.
+#' @param snpEff `r rd_cmd("snpEff")`.
+#' @seealso
+#' - <https://pcingola.github.io/SnpEff/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+snpEff <- make_command(
+  "snpEff",
+  function(subcmd = NULL, ..., snpEff = NULL) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(snpEff, allow_empty = FALSE, allow_null = TRUE)
+    SnpEff$new(cmd = snpEff, ..., subcmd = subcmd)
+  }
+)
+
+SnpEff <- R6Class(
+  "SnpEff",
+  inherit = Command,
+  private = list(
+    alias = function() "snpEff",
+    setup_help_params = function() "help",
+    combine_params = function(subcmd) {
+      if (private$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 7ad66ff..2d073f8 100644
--- a/man/allele_counter.Rd
+++ b/man/allele_counter.Rd
@@ -56,6 +56,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/bcftools.Rd b/man/bcftools.Rd
index ef1c8f4..f117b3b 100644
--- a/man/bcftools.Rd
+++ b/man/bcftools.Rd
@@ -46,6 +46,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()}
 }
 \concept{command}
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
index 3d58a79..7303c4b 100644
--- a/man/cellranger.Rd
+++ b/man/cellranger.Rd
@@ -60,6 +60,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/conda.Rd b/man/conda.Rd
index a77cd79..795924d 100644
--- a/man/conda.Rd
+++ b/man/conda.Rd
@@ -41,6 +41,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/exec.Rd b/man/exec.Rd
index 24363a5..6484778 100644
--- a/man/exec.Rd
+++ b/man/exec.Rd
@@ -34,6 +34,7 @@ Invoke a System Command
 \item \code{\link[=python]{python()}}
 \item \code{\link[=samtools]{samtools()}}
 \item \code{\link[=seqkit]{seqkit()}}
+\item \code{\link[=snpEff]{snpEff()}}
 \item \code{\link[=trust4]{trust4()}}
 \item \code{\link[=varscan]{varscan()}}
 }
diff --git a/man/fastp.Rd b/man/fastp.Rd
index fe62c54..30e8af8 100644
--- a/man/fastp.Rd
+++ b/man/fastp.Rd
@@ -45,6 +45,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
index a424b25..45e862d 100644
--- a/man/fastq_pair.Rd
+++ b/man/fastq_pair.Rd
@@ -66,6 +66,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
index 6b919ef..5e1ce8e 100644
--- a/man/gistic2.Rd
+++ b/man/gistic2.Rd
@@ -63,6 +63,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
index 13f460c..e7ada66 100644
--- a/man/kraken2.Rd
+++ b/man/kraken2.Rd
@@ -69,6 +69,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
index a0f820f..abe27bc 100644
--- a/man/kraken_tools.Rd
+++ b/man/kraken_tools.Rd
@@ -45,6 +45,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/perl.Rd b/man/perl.Rd
index 48c2918..5c7b2a3 100644
--- a/man/perl.Rd
+++ b/man/perl.Rd
@@ -42,6 +42,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
index 4a815b4..87ae0c1 100644
--- a/man/pyscenic.Rd
+++ b/man/pyscenic.Rd
@@ -42,6 +42,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/python.Rd b/man/python.Rd
index 5470219..8974f0b 100644
--- a/man/python.Rd
+++ b/man/python.Rd
@@ -42,6 +42,7 @@ Other \code{commands}:
 \code{\link{pyscenic}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/samtools.Rd b/man/samtools.Rd
index b2af24c..8167e4b 100644
--- a/man/samtools.Rd
+++ b/man/samtools.Rd
@@ -44,6 +44,7 @@ Other \code{commands}:
 \code{\link{pyscenic}()},
 \code{\link{python}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
index c753423..bae359f 100644
--- a/man/seqkit.Rd
+++ b/man/seqkit.Rd
@@ -42,6 +42,7 @@ Other \code{commands}:
 \code{\link{pyscenic}()},
 \code{\link{python}()},
 \code{\link{samtools}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()},
 \code{\link{varscan}()}
 }
diff --git a/man/snpEff.Rd b/man/snpEff.Rd
new file mode 100644
index 0000000..6c6a500
--- /dev/null
+++ b/man/snpEff.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cmd-snpEff.R
+\name{snpEff}
+\alias{snpEff}
+\title{Genetic variant annotation, and functional effect prediction toolbox.
+It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).}
+\usage{
+snpEff(subcmd = NULL, ..., snpEff = NULL)
+}
+\arguments{
+\item{subcmd}{Sub-Command of snpEff. Details see: \code{cmd_help(snpEff())}.}
+
+\item{...}{<\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \code{snpEff} 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(snpEff())}.}
+
+\item{snpEff}{A string of path to \code{snpEff} command.}
+}
+\value{
+A \code{command} object.
+}
+\description{
+Genetic variant annotation, and functional effect prediction toolbox.
+It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
+}
+\seealso{
+\itemize{
+\item \url{https://pcingola.github.io/SnpEff/}
+\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{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{trust4}()}
+}
+\concept{command}
diff --git a/man/trust4.Rd b/man/trust4.Rd
index a40463c..cf3e019 100644
--- a/man/trust4.Rd
+++ b/man/trust4.Rd
@@ -98,6 +98,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{varscan}()}
 }
 \concept{command}