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diff --git a/README.md b/README.md
@@ -7,5 +7,3 @@
 This is a package to perform Ghost Knockoff analysis for summary statistics data. 
 
 :warning: **Package is in early phase of development**. 
-
-:warning: **This package currently only works on Julia v1.8.x or 1.9.x** with Linux aarch64 or x86_64. If you need it to work on a different Julia version, please file an issue. 
diff --git a/docs/src/man/FAQ.ipynb b/docs/src/man/FAQ.ipynb
@@ -0,0 +1,32 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Common questions and Answers\n",
+    "\n",
+    "Here is a collection of common questions & answers. If you have a question not listed here, do not hesitate to open a new issue on Github. \n",
+    "\n",
+    "## How to handle missing data?\n",
+    "\n",
+    "## Memory requirement?"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.9.1",
+   "language": "julia",
+   "name": "julia-1.9"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.9.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/docs/src/man/FAQ.md b/docs/src/man/FAQ.md
@@ -0,0 +1,8 @@
+
+# Common questions and Answers
+
+Here is a collection of common questions & answers. If you have a question not listed here, do not hesitate to open a new issue on Github. 
+
+## How to handle missing data?
+
+## Memory requirement?
diff --git a/docs/src/man/developer.ipynb b/docs/src/man/developer.ipynb
@@ -36,6 +36,10 @@
     "Pkg.add(url=\"https://github.com/biona001/GhostKnockoffGWAS\")\n",
     "```\n",
     "\n",
+    "!!! warning\n",
+    "\n",
+    "    This package currently only works on Julia 1.8.x and 1.9.x. If you need it to work on a different Julia version, let us know by filing an issue on Github. \n",
+    "\n",
     "### Julia API\n",
     "\n",
     "```@autodocs\n",

diff --git a/docs/src/man/developer.md b/docs/src/man/developer.md
@@ -23,6 +23,10 @@ Pkg.add(url="https://github.com/biona001/Ghostbasil.jl")
 Pkg.add(url="https://github.com/biona001/GhostKnockoffGWAS")
 ```
 
+!!! warning
+
+    This package currently only works on Julia 1.8.x and 1.9.x. If you need it to work on a different Julia version, let us know by filing an issue on Github. 
+
 ### Julia API
 
 ```@autodocs

diff --git a/docs/src/man/examples.ipynb b/docs/src/man/examples.ipynb
@@ -0,0 +1,28 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Examples\n",
+    "\n",
+    "This page collect examples of running the ghost knockoff pipeline. We will cover topics such as installation, examining input data, running the software, and visualizing the output. "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.9.1",
+   "language": "julia",
+   "name": "julia-1.9"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.9.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/docs/src/man/examples.md b/docs/src/man/examples.md
@@ -0,0 +1,4 @@
+
+# Examples
+
+This page collect examples of running the ghost knockoff pipeline. We will cover topics such as installation, examining input data, running the software, and visualizing the output. 
diff --git a/docs/src/man/getting_started.ipynb b/docs/src/man/getting_started.ipynb
@@ -29,7 +29,39 @@
     "\n",
     "To see required inputs (and optional inputs), invoke\n",
     "```shell\n",
-    "./GhostKnockoffGWAS --help\n",
+    "$ ./GhostKnockoffGWAS --help\n",
+    "\n",
+    "usage: <PROGRAM> [--genome-build GENOME-BUILD] [--m M] [--seed SEED]\n",
+    "                 [-h] zfile knockoff_dir Neffect out\n",
+    "\n",
+    "positional arguments:\n",
+    "  zfile                 Tab or comma separated summary Z-score file.\n",
+    "                        The first row must be a header line that\n",
+    "                        contains CHR/POS/REF/ALT fields, as well as\n",
+    "                        something that indicates Z-score information.\n",
+    "                        CHR must be integer valued (e.g. chr21 is not\n",
+    "                        correct). If a column with `Z` is available,\n",
+    "                        it will be used as Z scores. Otherwise, we\n",
+    "                        need both `pvalue` and `beta` to be available,\n",
+    "                        or both `OR` (odds ratio) and `SE` (standard\n",
+    "                        error) to be available. In these cases, we\n",
+    "                        will convert them to Z scores.\n",
+    "  knockoff_dir          Path to the directory storing pre-processed\n",
+    "                        knockoff files\n",
+    "  Neffect               Effective sample size for original data (type:\n",
+    "                        Int64)\n",
+    "  out                   Output file prefix (without extensions)\n",
+    "\n",
+    "optional arguments:\n",
+    "  --genome-build GENOME-BUILD\n",
+    "                        Specifies the human genome build for the\n",
+    "                        summary file. Must be 19 (hg19) or 38 (hg38).\n",
+    "                        (type: Int64, default: 38)\n",
+    "  --m M                 Number of knockoffs to generate (type: Int64,\n",
+    "                        default: 5)\n",
+    "  --seed SEED           Sets the random seed (type: Int64, default:\n",
+    "                        2023)\n",
+    "  -h, --help            show this help message and exit\n",
     "```\n",
     "\n",
     "Example run:\n",

diff --git a/docs/src/man/getting_started.md b/docs/src/man/getting_started.md
@@ -24,7 +24,39 @@ Most users are expected to follow this workflow. For advanced users, see [Develo
 
 To see required inputs (and optional inputs), invoke
 ```shell
-./GhostKnockoffGWAS --help
+$ ./GhostKnockoffGWAS --help
+
+usage: <PROGRAM> [--genome-build GENOME-BUILD] [--m M] [--seed SEED]
+                 [-h] zfile knockoff_dir Neffect out
+
+positional arguments:
+  zfile                 Tab or comma separated summary Z-score file.
+                        The first row must be a header line that
+                        contains CHR/POS/REF/ALT fields, as well as
+                        something that indicates Z-score information.
+                        CHR must be integer valued (e.g. chr21 is not
+                        correct). If a column with `Z` is available,
+                        it will be used as Z scores. Otherwise, we
+                        need both `pvalue` and `beta` to be available,
+                        or both `OR` (odds ratio) and `SE` (standard
+                        error) to be available. In these cases, we
+                        will convert them to Z scores.
+  knockoff_dir          Path to the directory storing pre-processed
+                        knockoff files
+  Neffect               Effective sample size for original data (type:
+                        Int64)
+  out                   Output file prefix (without extensions)
+
+optional arguments:
+  --genome-build GENOME-BUILD
+                        Specifies the human genome build for the
+                        summary file. Must be 19 (hg19) or 38 (hg38).
+                        (type: Int64, default: 38)
+  --m M                 Number of knockoffs to generate (type: Int64,
+                        default: 5)
+  --seed SEED           Sets the random seed (type: Int64, default:
+                        2023)
+  -h, --help            show this help message and exit
 ```
 
 Example run:

diff --git a/src/app.jl b/src/app.jl
@@ -6,11 +6,11 @@ function julia_main()::Cint
             parse_commandline()
 
         println("Running GhostKnockoffGWAS analysis with the following options:")
-        println("zfile = $zfile")
-        println("knockoff_dir = $knockoff_dir")
+        println("zfile = $(abspath(zfile))")
+        println("knockoff_dir = $(abspath(knockoff_dir))")
         println("N (effective sample size) = $Neffect")
         println("hg_build = $hg_build")
-        println("outfile = $outfile")
+        println("outfile = $(abspath(outfile))")
         println("m (number of knockoffs for stability) = $m")
         println("seed = $seed")
 

diff --git a/src/utilities.jl b/src/utilities.jl
@@ -150,7 +150,7 @@ function read_zscores(filepath::String)
         pos = info[!, "POS"] |> Vector{Int}
         effect_allele = info[!, "ALT"] |> Vector{String}
         non_effect_allele = info[!, "REF"] |> Vector{String}
-        return chr, pos, effect_allele, non_effect_allele
+        chr, pos, effect_allele, non_effect_allele
     catch
         error("Z score file does not contain CHR/POS/REF/ALT.")
     end
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,5 +7,3 @@
		This is a package to perform Ghost Knockoff analysis for summary statistics data.

		:warning: Package is in early phase of development.

		:warning: This package currently only works on Julia v1.8.x or 1.9.x with Linux aarch64 or x86_64. If you need it to work on a different Julia version, please file an issue.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,4 @@

		# Examples

		This page collect examples of running the ghost knockoff pipeline. We will cover topics such as installation, examining input data, running the software, and visualizing the output.