diff --git a/.test/config_ecoli/config.yaml b/.test/config_ecoli/config.yaml
index eae0a1b..7bfff2e 100644
--- a/.test/config_ecoli/config.yaml
+++ b/.test/config_ecoli/config.yaml
@@ -37,10 +37,10 @@ settings:
   # ----------------------------------------------------------------------
 
   kmers_gwas:
-    # TODO Convert kmers table to PLINK 
-    # PLINK-conversion:
-    # # Set to true in order to convert k-mers table to PLINK format (.bed)
-    #   activate: false
+    # Convert kmers table to PLINK .bed format
+    kmers_table_to_bed:
+    # Set to true in order to convert k-mers table to PLINK format (.bed)
+      activate: true
 
     use_kmers_kinship:
     # Set to true in order to use k-mers based kinship matrix
@@ -167,13 +167,39 @@ params:
     extra: ""
 
   # ----------------------------------------------------------------------
-  #     merge_kemrs
+  #     merge_kmers Params
   # ----------------------------------------------------------------------
   
   merge_kmers:
     # Number of threads for kmc
     threads: 8
     
+  # ----------------------------------------------------------------------
+  #     convert_kmers_table_to_plink Params
+  # ----------------------------------------------------------------------
+
+  kmers_table_to_bed:
+    # Phenotypes to use (based on the phenos.tsv file)
+    # Only the individuals that exist in the given 
+    # phenotype file will be used
+    phenos: ["resistence"]
+    # Number of threads for kmers_table_to_bed
+    threads: 32
+    # k-mer length (should be between 15-31)
+    kmer_len: 31
+    # Minor allele count
+    # (Default is: 5)
+    minor_allele_count: 5
+    # Minor allele frequency 
+    # (Default is: 0.05)
+    minor_allele_freq: 0.05
+    # Maximal number of variants in each PLINK bed file
+    # Set by -b option
+    # Use a very large number if you want to avoid splitting
+    max_num_var: 10000000000
+    # Set to true in order to keep only unique presence/absence patterns
+    only_unique: true 
+
   # ----------------------------------------------------------------------
   #     kmersGWAS Params
   # ----------------------------------------------------------------------
@@ -192,9 +218,6 @@ params:
     # Minor allele frequency 
     # (Default is: 0.05)
     minor_allele_freq: 0.05
-    
-    # Maximal number of variants in each PLINK bed file
-    max_num_var: 10000000
 
     # Number of k-mers to filter from first step 
     # (Default is: 10001)
diff --git a/config/config.yaml b/config/config.yaml
index 35eaa1c..77434e8 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -37,10 +37,10 @@ settings:
   # ----------------------------------------------------------------------
 
   kmers_gwas:
-    # TODO Convert kmers table to PLINK 
-    # PLINK-conversion:
+    # Convert kmers table to PLINK .bed format
+    kmers_table_to_bed:
     # Set to true in order to convert k-mers table to PLINK format (.bed)
-    #   activate: false
+      activate: false
 
     use_kmers_kinship:
     # Set to true in order to use k-mers based kinship matrix
@@ -163,16 +163,42 @@ params:
     # counted. This parameter depends on the coverage, but should be
     # the same for all the individuals.
     count_thresh: 2
-
+    # Additional parameters for kmc
     extra: ""
 
   # ----------------------------------------------------------------------
-  #     merge_kmers
+  #     merge_kmers Params
   # ----------------------------------------------------------------------
   
   merge_kmers:
     # Number of threads for kmc
     threads: 8
+  
+  # ----------------------------------------------------------------------
+  #     convert_kmers_table_to_plink Params
+  # ----------------------------------------------------------------------
+
+  kmers_table_to_bed:
+    # Phenotypes to use (based on the phenos.tsv file)
+    # Only the individuals that exist in the given 
+    # phenotype file will be used
+    phenos: ["resistence"]
+    # Number of threads for kmers_table_to_bed
+    threads: 32
+    # k-mer length (should be between 15-31)
+    kmer_len: 31
+    # Minor allele count
+    # (Default is: 5)
+    minor_allele_count: 5
+    # Minor allele frequency 
+    # (Default is: 0.05)
+    minor_allele_freq: 0.05
+    # Maximal number of variants in each PLINK bed file
+    # Set by -b option
+    # Use a very large number if you want to avoid splitting
+    max_num_var: 10000000
+    # Set to true in order to keep only unique presence/absence patterns
+    only_unique: true 
 
   # ----------------------------------------------------------------------
   #     kmersGWAS Params
@@ -192,9 +218,6 @@ params:
     # Minor allele frequency 
     # (Default is: 0.05)
     minor_allele_freq: 0.05
-    
-    # Maximal number of variants in each PLINK bed file
-    max_num_var: 10000000
 
     # Number of k-mers to filter from first step 
     # (Default is: 10001)
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 582de0d..0f60f0a 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -144,17 +144,21 @@ KMERSGWAS_BIN_PATH = os.path.join(KMERSGWAS_DIR, "bin/")
 #     Common Helper Functions
 # =================================================================================================
 
-def sra_only(sample, library):
+# Check if the sample is SRA only
+def sra_only(sample, library): 
     return pd.isnull(samples.loc[(sample, library), "fq1"]) and pd.isnull(samples.loc[(sample, library), "fq2"]) \
            and not pd.isnull(samples.loc[(sample, library), "sra"])
 
-def is_sra_se(sample, library):
+# Check if the sample is SRA only and single-end
+def is_sra_se(sample, library): 
     return sra_only(sample, library) and config["settings"]["single_end"]
 
-def is_sra_pe(sample, library):
+# Check if the sample is SRA only and paired-end
+def is_sra_pe(sample, library): 
     return sra_only(sample, library) and not config["settings"]["single_end"]
 
-def get_individual_fastq(wildcards):
+# Get individual FASTQ files
+def get_individual_fastq(wildcards): 
 # Adapted from: https://github.com/snakemake-workflows/chipseq
     """Get individual raw FASTQ files from samples sheet."""
     fastqs = samples.loc[(wildcards.sample, wildcards.library), ["fq1", "fq2"]].dropna()
@@ -174,7 +178,8 @@ def get_individual_fastq(wildcards):
         else:
             return samples.loc[ (wildcards.sample, wildcards.library), "fq2" ]
 
-def get_fastqs(wildcards):
+# Get FASTQ files
+def get_fastqs(wildcards): 
 # Adapted from: https://github.com/snakemake-workflows/chipseq
     """Get raw FASTQ files from samples sheet."""
     fastqs = samples.loc[(wildcards.sample, wildcards.library), ["fq1", "fq2"]].dropna()
@@ -190,6 +195,7 @@ def get_fastqs(wildcards):
         u = samples.loc[ (wildcards.sample, wildcards.library), ["fq1", "fq2"] ].dropna()
         return [ f"{u.fq1}", f"{u.fq2}" ]
 
+# Check if FASTQ files are gzipped
 def ends_with_gz(samp_tab):
     fqs = samp_tab.loc[:, ['fq1']]
     if not pd.isnull(fqs.fq1).all():
@@ -200,7 +206,8 @@ def ends_with_gz(samp_tab):
     else:
         return False
 
-def get_multiqc_input(wildcards):
+# Get MultiQC input
+def get_multiqc_input(wildcards): 
     """Get multiqc input."""
     multiqc_input = []
     multiqc_input.extend(
@@ -222,18 +229,12 @@ def get_multiqc_input(wildcards):
         )
     return multiqc_input
 
-def get_phenos(wildcards):
+# Get phenotypes
+def get_phenos(wildcards): 
     """Get fastq files using samples sheet."""
     pheno_names = phenos.loc[(wildcards.pheno), ["pheno_path"]].dropna()
     return {"pheno_path": pheno_names.pheno_path}
 
-def get_input_path_for_generate_input_lists():
-    """Get input path of reads to create input lists."""
-    if config["settings"]["trimming"]["activate"]:
-        return "results/trimmed"
-    else:
-        return "results/reads"
-
 def get_plink_prefix():
     """Get prefix fopr the SNPs plink file."""
     plink_path = config["settings"]["kmers_gwas"]["use_snps_kinship"]["snps_plink"]
@@ -289,18 +290,25 @@ def get_target_output(wildcards):
     Get all requested inputs (target outputs) for rule all.
     """
 
-    align_kmers = config["settings"]["align_kmers"]["activate"]
-    align_reads_with_kmers = config["settings"]["align_reads_with_kmers"]["activate"]
-    assemble_reads_with_kmers = config["settings"]["assemble_reads"]["activate"]
-    blast_assembled_reads = config["settings"]["blast_contigs"]["activate"]
+    # Activate/Deactivate rules
+    align_kmers = config["settings"]["align_kmers"]["activate"] # Activate align kmers
+    align_reads_with_kmers = config["settings"]["align_reads_with_kmers"]["activate"] # Activate align reads with kmers
+    assemble_reads_with_kmers = config["settings"]["assemble_reads"]["activate"] # Activate assemble reads with kmers
+    blast_assembled_reads = config["settings"]["blast_contigs"]["activate"] # Activate BLAST assembled reads
+    convert_kmers_table_to_plink = config["settings"]["kmers_gwas"]["kmers_table_to_bed"]["activate"] # Activate convert kmers table to plink
 
-    target_output = []
+    target_output = [] # List of target outputs
 
+    ### Add target outputs for rule all ###
+    
+    # MultiQC
     target_output.extend(
         expand(
             "results/qc/multiqc.html"
         )
     ),
+
+    # KMC, k-mers stats
     target_output.extend(
         expand(
             [
@@ -313,11 +321,25 @@ def get_target_output(wildcards):
             ]
         )
     ),
+
+    # Combine and filter k-mers
     target_output.extend(
         expand(
             "results/plots/kmers_list/kmer_allele_counts.pdf"
         )
     ),
+
+    #  Convert the k-mers table to PLINK
+    if convert_kmers_table_to_plink: 
+        # If convert_kmers_table_to_plink is activated
+        target_output.extend(
+            expand(
+               "results/kmers_table/plink/pheno_{pheno}/convert_kmers_table_to_plink.done",
+                pheno= config["params"]["kmers_table_to_bed"]["phenos"]
+            )
+        ),
+
+    # kmersGWAS
     target_output.extend(
         expand(
             "results/kmers_gwas/{pheno}/kmers/pass_threshold_5per",
@@ -325,6 +347,7 @@ def get_target_output(wildcards):
         )
     ),
 
+    # Align k-mers
     if align_kmers:
         target_output.extend(
             expand(
@@ -332,6 +355,7 @@ def get_target_output(wildcards):
             )
         ),
     
+    # Align reads with k-mers
     if align_reads_with_kmers:
         target_output.extend(
             expand(
@@ -339,6 +363,7 @@ def get_target_output(wildcards):
             )
         ),
 
+    # Assemble reads with k-mers
     if assemble_reads_with_kmers:
         target_output.extend(
             expand(
@@ -346,6 +371,7 @@ def get_target_output(wildcards):
             )
         ),
 
+    # BLAST assembled reads
     if blast_assembled_reads:
         target_output.extend(
             expand(
@@ -353,6 +379,7 @@ def get_target_output(wildcards):
             )
         ),
 
+    # Return target outputs
     return target_output
 
 # =================================================================================================
\ No newline at end of file
diff --git a/workflow/rules/generate_kmers_table.smk b/workflow/rules/generate_kmers_table.smk
index 8cc1061..e5c8a5b 100644
--- a/workflow/rules/generate_kmers_table.smk
+++ b/workflow/rules/generate_kmers_table.smk
@@ -29,5 +29,44 @@ rule create_kmers_table:
         """
 
 # =================================================================================================
-#     TODO: Convert the k-mers table to PLINK binary file
+#     Convert the k-mers table to PLINK binary file
+# =================================================================================================
+
+rule convert_kmers_table_to_plink:
+    input:
+        kmers_table = "results/kmers_table/kmers_table.table",
+        phenotype = lambda wildcards: phenos.loc[(wildcards.pheno), ["pheno_path"]],
+        kmersGWAS_bin = rules.extract_kmersGWAS.output.kmersGWAS_bin,
+    output:
+        bed = "results/kmers_table/plink/pheno_{pheno}/kmers_table.presence_absence.0.bed",
+        done = touch("results/kmers_table/plink/pheno_{pheno}/convert_kmers_table_to_plink.done"),
+    params:
+        input_prefix = lambda w, input: os.path.splitext(input.kmers_table)[0],
+        output_prefix = lambda w, output: os.path.splitext(output.bed)[0].rsplit(".", 1)[0],
+        kmer_len = config["params"]["kmers_table_to_bed"]["kmer_len"],
+        max_num_var = config["params"]["kmers_table_to_bed"]["max_num_var"],
+        mac = config["params"]["kmers_table_to_bed"]["minor_allele_count"],
+        maf = config["params"]["kmers_table_to_bed"]["minor_allele_freq"],
+        only_unique = "-u" if config["params"]["kmers_table_to_bed"]["only_unique"] else "",
+    conda:
+        "../envs/kmers_gwas.yaml"
+    log:
+        "logs/create_kmers_table/convert_kmers_table_to_plink.pheno_{pheno}.log"
+    message:
+        "Converting the k-mers table to PLINK binary file..."
+    shell:
+        """
+        export LD_LIBRARY_PATH=$CONDA_PREFIX/lib
+        
+        {input.kmersGWAS_bin}/kmers_table_to_bed \
+        -t {params.input_prefix} \
+        -p {input.phenotype} \
+        -o {params.output_prefix} \
+        -k {params.kmer_len} \
+        --maf {params.maf} --mac {params.mac} \
+        -b {params.max_num_var} \
+        {params.only_unique} \
+        >>{log} 2>&1
+        """
+
 # =================================================================================================
\ No newline at end of file