diff --git a/README.md b/README.md
index fec96e2466dd17b76f2adaaf94f53f4ec012d9a0..c169f13e95a6ea84daedbae59460d2c365324cc3 100755
--- a/README.md
+++ b/README.md
@@ -146,7 +146,7 @@ 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/modules/modkit.nf b/src/modules/modkit.nf
index d9549373aec63153ac06499c28b6cb393f5075df..d39eddebeef9eeb96054342ea398259d4e3201e8 100755
--- a/src/modules/modkit.nf
+++ b/src/modules/modkit.nf
@@ -14,15 +14,48 @@ process MODKIT {
 
     script:
         """
-        echo "starting modkit"
+        echo "starting probabilities calculation"
+        ## Inspect base modification probabilities
+        modkit sample-probs --hist \
+            --threads ${modkit_threads} \
+            --interval-size ${modkit_isize} \
+            --only-mapped \
+            --region MT \
+            --out-dir "./modkit_prob/" "${bam}"
+        echo "modification prob. calculated"
+        echo "starting modkit extract calls"
         ## Make Methylation TSV file
-        modkit extract full --bgzf --queue-size ${modkit_extract_qsize} --threads ${modkit_threads} --interval-size ${modkit_isize} --mapped-only "${bam}" "${id}_modkit_output.tsv"
+        modkit extract full --bgzf \
+            --queue-size ${modkit_extract_qsize} \
+            --threads ${modkit_threads} \
+            --interval-size ${modkit_isize} \
+            --region MT \
+            --mapped-only \
+            "${bam}" "${id}_modkit_full.tsv.gz"
         echo "extract successful"
         ## Make Methylation Table (--chunk-size is a multiplier of threads, 1.5x by default)
-        modkit pileup --threads ${modkit_threads} --interval-size ${modkit_isize} "${bam}" "${id}_modkit_pileup.bed" --log-filepath "${id}_modkit_pileup.log"
+        modkit pileup --threads ${modkit_threads} \
+            --interval-size ${modkit_isize} \
+            --region MT \
+            --filter-threshold C:0.75 \
+            --filter-threshold A:0.75 \
+            --mod-thresholds m:0.75 \
+            --mod-thresholds h:0.75 \
+            --mod-thresholds a:0.75 \
+            "${bam}" "${id}_modkit_pileup.bed" \
+            --log-filepath "${id}_modkit_pileup.log"
         echo "pileup successful"
         ## Make Summary
-        modkit summary --threads ${modkit_threads} --interval-size ${modkit_isize} ${bam}  > "${id}_modkit_summary.txt"
+        modkit summary --only-mapped \
+            --threads ${modkit_threads} \
+            --interval-size ${modkit_isize} \
+            --region MT \
+            --filter-threshold C:0.75 \
+            --filter-threshold A:0.75 \
+            --mod-thresholds m:0.75 \
+            --mod-thresholds h:0.75 \
+            --mod-thresholds a:0.75 \
+        ${bam}  > "${id}_modkit_summary.txt"
         echo "summary successful"
         """
-}
+}
\ No newline at end of file
diff --git a/src/nextflow.config b/src/nextflow.config
index 79873970d8f2d700a3030df66701a3e7b0fe39d8..e7b10a71ebeb24a7920b34e720ea5b201a75fc2e 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -22,7 +22,7 @@ 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