diff --git a/README.md b/README.md
index 47834be970c7b3e85fedd6048e2b7ff4253f5c18..76f10170ee53c2043fd778bb18cc2ba80c5e8cc4 100755
--- a/README.md
+++ b/README.md
@@ -138,7 +138,7 @@ Many of the parameters for this step are based on dorado basecaller, see their [
 ```txt
 --basecall_mods
 
-<Type: String. Comma separated list of base modifications you want to basecall. See dorado docs for more information. Please note that you can't use more than one modification per nucleotide. Options: "4mC_5mC", "5mCG_5hmCG", "5mC_5hmC", "6mA". Default: "5mC_5hmC">
+<Type: String. Comma separated list of base modifications you want to basecall. See dorado docs for more information. Please note that you can't use more than one modification per nucleotide. Options: "4mC_5mC", "5mCG_5hmCG", "5mC_5hmC", "6mA". Default: "5mC_5hmC,6mA">
 ```
 
 ```txt
diff --git a/parameters/human_blood/modkit.yaml b/parameters/human_blood/modkit.yaml
index 5149ad894bc1204d3e42e2a5579b0d4274dcaa6e..3a694f0d54cf2ad28e2bcf93b1ed0bc5fd91fab1 100644
--- a/parameters/human_blood/modkit.yaml
+++ b/parameters/human_blood/modkit.yaml
@@ -1,4 +1,5 @@
 project_name: "results_human_blood"
 step: 3
 steps_2_and_3_input_directory: "./results/results_human_blood/"
+reference_file: "./references/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
 out_dir: "results_human_blood/"
\ No newline at end of file
diff --git a/src/main.nf b/src/main.nf
index d38bd5e9a79f76d9d661ec903de132c9c37a42e1..25986bb409a974a75e10d1130aff64e6663d2549 100755
--- a/src/main.nf
+++ b/src/main.nf
@@ -85,6 +85,7 @@ workflow {
         quality_thresholds = Channel.fromPath("${params.steps_2_and_3_input_directory}/intermediate_qc_reports/quality_score_thresholds/*")
         multiqc_config = Channel.fromPath(params.multiqc_config)
         multiqc_input = Channel.fromPath("${params.steps_2_and_3_input_directory}/multiqc_input/**", type: "file")
+        reference_file = file(params.reference_file)
     }
     // Run steps
     if (params.step.toString() == "1") {
@@ -94,6 +95,6 @@ workflow {
     } else if (params.step.toString() == "2_from_minknow") {
         FILTERING_AND_QC_FROM_MINKNOW(input_dir, mapq, qscore_thresh)
     } else if (params.step.toString()== "3") {
-        MODKIT_AND_MULTIQC(filtered_bams, filtered_bais, num_reads, read_length, quality_thresholds, multiqc_config, multiqc_input)
+        MODKIT_AND_MULTIQC(filtered_bams, filtered_bais, num_reads, read_length, quality_thresholds, multiqc_config, multiqc_input, reference_file)
     }
 }
diff --git a/src/modules/modkit.nf b/src/modules/modkit.nf
index d5a1a9da7165b85c6b8f7384be697ae5f4ab7625..34dc67e855abbb5c5ceb539fae3fdb5408da014c 100755
--- a/src/modules/modkit.nf
+++ b/src/modules/modkit.nf
@@ -5,21 +5,43 @@ process MODKIT {
     input:
         tuple val(id), path(bam)
         path bai
+        path reference_file
 
     output:
         path "*"
 
     script:
         """
-        echo "starting modkit"
+       echo "starting probabilities calculation"
+        ## Inspect base modification probabilities
+        modkit sample-probs --hist -t 4 -i 10000 \
+        --out-dir "./modkit_prob/" "${bam}"
+        echo "modification prob. calculated"
+        
+        echo "starting modkit extract calls"
         ## Make Methylation TSV file
-        modkit extract full --bgzf --queue-size 1000 -t 4 -i 10000 --mapped-only "${bam}" "${id}_modkit_output.tsv"
+        modkit extract calls --bgzf --queue-size 1000 -t 4 -i 10000 \
+        --reference "${reference_file}" \
+        --filter-threshold 0.9 \
+        --mapped-only \
+        --region MT \
+        "${bam}" "${id}_modkit_calls.tsv"
         echo "extract successful"
+
         ## Make Methylation Table
-        modkit pileup -t 4 -i 10000 --chunk-size 4 "${bam}" "${id}_modkit_pileup.bed" --log-filepath "${id}_modkit_pileup.log"
+        modkit pileup -t 4 -i 10000 \
+        --filter-threshold 0.9 \
+        --region MT \
+        --sample-region MT \
+        "${bam}" "${id}_modkit_pileup.bed" \
+        --log-filepath "${id}_modkit_pileup.log"
         echo "pileup successful"
+        
         ## Make Summary
-        modkit summary -i 10000 ${bam}  > "${id}_modkit_summary.txt"
+        modkit summary -t 4 -i 10000 \
+        --filter-threshold 0.9 \
+        --region MT \
+        ${bam}  > "${id}_modkit_summary.txt"
         echo "summary successful"
         """
 }
diff --git a/src/nextflow.config b/src/nextflow.config
index 41d22397149db2cd972c6cbea2069d6c26aa7051..a8d5c388ce1194666bed3b4071d4163ef1fdb335 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -19,7 +19,7 @@ params {
     // Desired basecall speed ("fast", "hac", "sup"; @latest <- latest version available)
     basecall_speed = "sup@latest"
     // Desired basecaller modifications (4mC_5mC, 5mCG_5hmCG, 5mC_5hmC, 6mA). Can't use more than one modification per nucleotide.
-    basecall_mods = "5mC_5hmC"
+    basecall_mods = "5mC_5hmC,6mA"
     // Kit name (kit used to barcode the samples (e.g. SQK-RBK114-24); Use "None" to skip --kit-name in basecalling)
     barcoding_kit = "SQK-RBK114-24"
     // Threshold for mapped reasds
diff --git a/src/sub_workflows/MODKIT_AND_MULTIQC.nf b/src/sub_workflows/MODKIT_AND_MULTIQC.nf
index 35294c78f20ee2aef614636017fef98b5f09af10..b6d77d36057abb9bd5978f5cc3fbd215ab30a13c 100755
--- a/src/sub_workflows/MODKIT_AND_MULTIQC.nf
+++ b/src/sub_workflows/MODKIT_AND_MULTIQC.nf
@@ -13,11 +13,12 @@ workflow MODKIT_AND_MULTIQC {
         quality_thresholds
         multiqc_config
         multiqc_input
+        reference_file
 
     main:
         CALCULATE_COVERAGE(filtered_bams, filtered_bais)
         MERGE_COVERAGE(CALCULATE_COVERAGE.out.collect())
         MERGE_QC_REPORT(num_reads.collect(), read_length.collect(), quality_thresholds.collect())
         MULTIQC(multiqc_input.concat(MERGE_QC_REPORT.out.flatten()).collect(), MERGE_COVERAGE.out.mqc, multiqc_config)
-        MODKIT(filtered_bams, filtered_bais)
+        MODKIT(filtered_bams, filtered_bais, reference_file)
 }