diff --git a/doc/plots/iGenVar_only/results.DEL.png b/doc/plots/iGenVar_only/results.DEL.png
index 0b08a4bf..ee332b74 100644
Binary files a/doc/plots/iGenVar_only/results.DEL.png and b/doc/plots/iGenVar_only/results.DEL.png differ
diff --git a/doc/plots/iGenVar_only/results.INS.png b/doc/plots/iGenVar_only/results.INS.png
index cccb12ad..0a982226 100644
Binary files a/doc/plots/iGenVar_only/results.INS.png and b/doc/plots/iGenVar_only/results.INS.png differ
diff --git a/doc/plots/iGenVar_only/results.all.png b/doc/plots/iGenVar_only/results.all.png
index e46a5681..cd36aeb3 100644
Binary files a/doc/plots/iGenVar_only/results.all.png and b/doc/plots/iGenVar_only/results.all.png differ
diff --git a/doc/plots/iGenVar_only/results.no_DUP_and_INV.png b/doc/plots/iGenVar_only/results.no_DUP_and_INV.png
index 69f61d2b..a3422c4d 100644
Binary files a/doc/plots/iGenVar_only/results.no_DUP_and_INV.png and b/doc/plots/iGenVar_only/results.no_DUP_and_INV.png differ
diff --git a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/callers.smk b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/callers.smk
index 300ba8e4..b37a14ed 100644
--- a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/callers.smk
+++ b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/callers.smk
@@ -1,4 +1,5 @@
-sample = config["parameters"]["sample"],
+sample_HG002 = config["parameters"]["sample_HG002"],
+sample_NA12878 = config["parameters"]["sample_NA12878"],
 min_var_length = config["parameters"]["min_var_length"],
 max_var_length = config["parameters"]["max_var_length"]
 
@@ -13,14 +14,28 @@ rule run_iGenVar:
             short_bam = config["short_read_bam"]["s1"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'S2': # Illumina Mate Pair
             short_bam = config["short_read_bam"]["s2"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
+                --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
+            """)
+        elif wildcards.input_combination == 'S3': # Illumina HiSeq
+            short_bam = config["short_read_bam"]["s3"]
+            shell("""
+            /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
+                --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
+            """)
+        elif wildcards.input_combination == 'S4': # NA12878 WGS GRCh38
+            short_bam = config["short_read_bam"]["s4"]
+            shell("""
+            /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
+                --output {output.vcf} --vcf_sample_name {sample_NA12878} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'S1L1': # Illumina Paired End & MtSinai PacBio
@@ -28,7 +43,7 @@ rule run_iGenVar:
             long_bam = config["long_read_bam"]["l1"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'S2L1': # Illumina Mate Pair & MtSinai PacBio
@@ -36,7 +51,15 @@ rule run_iGenVar:
             long_bam = config["long_read_bam"]["l1"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
+                --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
+            """)
+        elif wildcards.input_combination == 'S3L1': # Illumina HiSeq & MtSinai PacBio
+            short_bam = config["short_read_bam"]["s3"],
+            long_bam = config["long_read_bam"]["l1"]
+            shell("""
+            /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'S1L2': # Illumina Paired End & PacBio CCS
@@ -44,7 +67,7 @@ rule run_iGenVar:
             long_bam = config["long_read_bam"]["l2"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'S2L2': # Illumina Mate Pair & PacBio CCS
@@ -52,7 +75,15 @@ rule run_iGenVar:
             long_bam = config["long_read_bam"]["l2"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
+                --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
+            """)
+        elif wildcards.input_combination == 'S3L2': # Illumina HiSeq & PacBio CCS
+            short_bam = config["short_read_bam"]["s3"],
+            long_bam = config["long_read_bam"]["l2"]
+            shell("""
+            /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'S1L3': # Illumina Paired End & 10X Genomics
@@ -60,7 +91,7 @@ rule run_iGenVar:
             long_bam = config["long_read_bam"]["l3"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'S2L3': # Illumina Mate Pair & 10X Genomics
@@ -68,56 +99,64 @@ rule run_iGenVar:
             long_bam = config["long_read_bam"]["l3"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
+                --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
+            """)
+        elif wildcards.input_combination == 'S3L3': # Illumina HiSeq & 10X Genomics
+            short_bam = config["short_read_bam"]["s3"],
+            long_bam = config["long_read_bam"]["l3"]
+            shell("""
+            /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} --input_long_reads {long_bam} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'L1': # MtSinai PacBio
             long_bam = config["long_read_bam"]["l1"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_long_reads {long_bam} \
-                 --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                 --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'L2': # PacBio CCS
             long_bam = config["long_read_bam"]["l2"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_long_reads {long_bam} \
-                 --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                 --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'L3': # 10X Genomics
             long_bam = config["long_read_bam"]["l3"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_long_reads {long_bam} \
-                 --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                 --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'hg38_Sim_default': # Illumina
             short_bam = config["simulated_short_read_bam"]["sim1"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'hg38_Sim_InDel': # Illumina
             short_bam = config["simulated_short_read_bam"]["sim2"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         elif wildcards.input_combination == 'hg38_Sim_noSNP': # Illumina
             short_bam = config["simulated_short_read_bam"]["sim3"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
-                --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         else: # wildcards.input_combination == 'hg38_Sim_SNPandSV': # Illumina
             short_bam = config["simulated_short_read_bam"]["sim4"]
             shell("""
             /usr/bin/time -v ./build/iGenVar/bin/iGenVar --input_short_reads {short_bam} \
-                 --output {output.vcf} --vcf_sample_name {sample} --threads {threads} \
+                 --output {output.vcf} --vcf_sample_name {sample_HG002} --threads {threads} \
                 --min_var_length {min_var_length} --max_var_length {max_var_length} --min_qual 1 &>> {log}
             """)
         # Defaults:
diff --git a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.DEL.smk b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.DEL.smk
index 9c97f2da..fecef7b8 100644
--- a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.DEL.smk
+++ b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.DEL.smk
@@ -30,8 +30,8 @@ rule truvari_DEL:
         "logs/truvari/truvari_output.{input_combination}.{min_qual}.log"
     params:
         output_dir = "results/caller_comparison_iGenVar_only/eval/{input_combination}/DEL.min_qual_{min_qual}",
-        truth_set_gz = config["truth_set_DEL_renamed_chr"]["gz"],
-        truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+        truth_set_gz = config["truth_set_HG002_DEL_renamed_chr"]["gz"],
+        truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
     shell:
         """
         rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
@@ -58,6 +58,10 @@ rule cat_truvari_results_DEL:
                       min_qual = min_qual_iGenVar),
         S2   = expand("results/caller_comparison_iGenVar_only/eval/S2/DEL.min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
+        S3   = expand("results/caller_comparison_iGenVar_only/eval/S3/min_qual_{min_qual}/pr_rec.txt",
+                      min_qual = min_qual_iGenVar),
+        # S4   = expand("results/caller_comparison_iGenVar_only/eval/S4/min_qual_{min_qual}/pr_rec.txt",
+        #               min_qual = min_qual_iGenVar),
         L1   = expand("results/caller_comparison_iGenVar_only/eval/L1/DEL.min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
         L2   = expand("results/caller_comparison_iGenVar_only/eval/L2/DEL.min_qual_{min_qual}/pr_rec.txt",
@@ -67,6 +71,8 @@ rule cat_truvari_results_DEL:
     output:
         S1   = temp("results/caller_comparison_iGenVar_only/eval/S1.DEL_results.txt"),
         S2   = temp("results/caller_comparison_iGenVar_only/eval/S2.DEL_results.txt"),
+        S3   = temp("results/caller_comparison_iGenVar_only/eval/S3.all_results.txt"),
+        # S4   = temp("results/caller_comparison_iGenVar_only/eval/S4.all_results.txt"),
         L1   = temp("results/caller_comparison_iGenVar_only/eval/L1.DEL_results.txt"),
         L2   = temp("results/caller_comparison_iGenVar_only/eval/L2.DEL_results.txt"),
         L3   = temp("results/caller_comparison_iGenVar_only/eval/L3.DEL_results.txt"),
@@ -75,10 +81,16 @@ rule cat_truvari_results_DEL:
     run:
         shell("cat {input.S1} > {output.S1}")
         shell("cat {input.S2} > {output.S2}")
+        shell("cat {input.S3} > {output.S3}")
+        # shell("cat {input.S4} > {output.S4}")
         shell("cat {input.L1} > {output.L1}")
         shell("cat {input.L2} > {output.L2}")
         shell("cat {input.L3} > {output.L3}")
         shell("""
-            cat {output.S1} {output.S2} \
+            cat {output.S1} {output.S2} {output.S3} \
                 {output.L1} {output.L2} {output.L3} > {output.all}
         """)
+        # shell("""
+        #     cat {output.S1} {output.S2} {output.S3} {output.S4} \
+        #         {output.L1} {output.L2} {output.L3} > {output.all}
+        # """)
diff --git a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.INS.smk b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.INS.smk
index 47421159..261ab916 100644
--- a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.INS.smk
+++ b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.INS.smk
@@ -30,8 +30,8 @@ rule truvari_INS:
         "logs/truvari/truvari_output.{input_combination}.{min_qual}.log"
     params:
         output_dir = "results/caller_comparison_iGenVar_only/eval/{input_combination}/INS.min_qual_{min_qual}",
-        truth_set_gz = config["truth_set_INS_renamed_chr"]["gz"],
-        truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+        truth_set_gz = config["truth_set_HG002_INS_renamed_chr"]["gz"],
+        truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
     shell:
         """
         rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
@@ -58,6 +58,10 @@ rule cat_truvari_results_INS:
                       min_qual = min_qual_iGenVar),
         S2   = expand("results/caller_comparison_iGenVar_only/eval/S2/INS.min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
+        S3   = expand("results/caller_comparison_iGenVar_only/eval/S3/min_qual_{min_qual}/pr_rec.txt",
+                      min_qual = min_qual_iGenVar),
+        # S4   = expand("results/caller_comparison_iGenVar_only/eval/S4/min_qual_{min_qual}/pr_rec.txt",
+        #               min_qual = min_qual_iGenVar),
         L1   = expand("results/caller_comparison_iGenVar_only/eval/L1/INS.min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
         L2   = expand("results/caller_comparison_iGenVar_only/eval/L2/INS.min_qual_{min_qual}/pr_rec.txt",
@@ -67,6 +71,8 @@ rule cat_truvari_results_INS:
     output:
         S1   = temp("results/caller_comparison_iGenVar_only/eval/S1.INS_results.txt"),
         S2   = temp("results/caller_comparison_iGenVar_only/eval/S2.INS_results.txt"),
+        S3   = temp("results/caller_comparison_iGenVar_only/eval/S3.all_results.txt"),
+        # S4   = temp("results/caller_comparison_iGenVar_only/eval/S4.all_results.txt"),
         L1   = temp("results/caller_comparison_iGenVar_only/eval/L1.INS_results.txt"),
         L2   = temp("results/caller_comparison_iGenVar_only/eval/L2.INS_results.txt"),
         L3   = temp("results/caller_comparison_iGenVar_only/eval/L3.INS_results.txt"),
@@ -75,10 +81,16 @@ rule cat_truvari_results_INS:
     run:
         shell("cat {input.S1} > {output.S1}")
         shell("cat {input.S2} > {output.S2}")
+        shell("cat {input.S3} > {output.S3}")
+        # shell("cat {input.S4} > {output.S4}")
         shell("cat {input.L1} > {output.L1}")
         shell("cat {input.L2} > {output.L2}")
         shell("cat {input.L3} > {output.L3}")
         shell("""
-            cat {output.S1} {output.S2} \
+            cat {output.S1} {output.S2} {output.S3} \
                 {output.L1} {output.L2} {output.L3} > {output.all}
         """)
+        # shell("""
+        #     cat {output.S1} {output.S2} {output.S3} {output.S4} \
+        #         {output.L1} {output.L2} {output.L3} > {output.all}
+        # """)
diff --git a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.no_DUP_and_INV.smk b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.no_DUP_and_INV.smk
index bfff251b..6c022452 100644
--- a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.no_DUP_and_INV.smk
+++ b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.no_DUP_and_INV.smk
@@ -57,8 +57,8 @@ rule no_DUP_and_INV_truvari:
         "logs/truvari/truvari_output.{input_combination}.{min_qual}.log"
     params:
         output_dir = "results/caller_comparison_iGenVar_only/eval/{input_combination}/no_DUP_and_INV.min_qual_{min_qual}",
-        truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-        truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+        truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+        truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
     shell:
         """
         rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
@@ -85,6 +85,10 @@ rule no_DUP_and_INV_cat_truvari_results_all:
                       min_qual = min_qual_iGenVar),
         S2   = expand("results/caller_comparison_iGenVar_only/eval/S2/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
+        S3   = expand("results/caller_comparison_iGenVar_only/eval/S3/min_qual_{min_qual}/pr_rec.txt",
+                      min_qual = min_qual_iGenVar),
+        # S4   = expand("results/caller_comparison_iGenVar_only/eval/S4/min_qual_{min_qual}/pr_rec.txt",
+        #               min_qual = min_qual_iGenVar),
         L1   = expand("results/caller_comparison_iGenVar_only/eval/L1/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
         L2   = expand("results/caller_comparison_iGenVar_only/eval/L2/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
@@ -94,6 +98,8 @@ rule no_DUP_and_INV_cat_truvari_results_all:
     output:
         S1   = temp("results/caller_comparison_iGenVar_only/eval/S1.no_DUP_and_INV_results.txt"),
         S2   = temp("results/caller_comparison_iGenVar_only/eval/S2.no_DUP_and_INV_results.txt"),
+        S3   = temp("results/caller_comparison_iGenVar_only/eval/S3.all_results.txt"),
+        # S4   = temp("results/caller_comparison_iGenVar_only/eval/S4.all_results.txt"),
         L1   = temp("results/caller_comparison_iGenVar_only/eval/L1.no_DUP_and_INV_results.txt"),
         L2   = temp("results/caller_comparison_iGenVar_only/eval/L2.no_DUP_and_INV_results.txt"),
         L3   = temp("results/caller_comparison_iGenVar_only/eval/L3.no_DUP_and_INV_results.txt"),
@@ -102,10 +108,16 @@ rule no_DUP_and_INV_cat_truvari_results_all:
     run:
         shell("cat {input.S1} > {output.S1}")
         shell("cat {input.S2} > {output.S2}")
+        shell("cat {input.S3} > {output.S3}")
+        # shell("cat {input.S4} > {output.S4}")
         shell("cat {input.L1} > {output.L1}")
         shell("cat {input.L2} > {output.L2}")
         shell("cat {input.L3} > {output.L3}")
         shell("""
-            cat {output.S1} {output.S2} \
+            cat {output.S1} {output.S2} {output.S3} \
                 {output.L1} {output.L2} {output.L3} > {output.all}
         """)
+        # shell("""
+        #     cat {output.S1} {output.S2} {output.S3} {output.S4} \
+        #         {output.L1} {output.L2} {output.L3} > {output.all}
+        # """)
diff --git a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.smk b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.smk
index 126baa40..603f875d 100644
--- a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.smk
+++ b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.smk
@@ -37,15 +37,18 @@ rule truvari:
     log:
         "logs/truvari/truvari_output.{input_combination}.{min_qual}.log"
     params:
-        output_dir = "results/caller_comparison_iGenVar_only/eval/{input_combination}/min_qual_{min_qual}",
-        truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-        truth_set_bed = config["truth_set_renamed_chr"]["bed"]
-    shell:
-        """
-        rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
-            --passonly --includebed {params.truth_set_bed} &>> {log}
-        """
-        # -f data/reference/hs37d5.fa
+        output_dir = "results/caller_comparison_iGenVar_only/eval/{input_combination}/min_qual_{min_qual}"
+    run:
+        if wildcards.input_combination == 'S4': # NA12878 WGS GRCh38
+            truth_set_gz = config["truth_set_NA12878"]["gz"],
+            truth_set_bed = config["truth_set_NA12878"]["bed"]
+        else:
+            truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+            truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
+        shell("""
+            rm -rf {params.output_dir} && truvari bench -b {truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
+                --passonly --includebed {truth_set_bed} &>> {log}
+        """)
 
 rule reformat_truvari_results:
     input:
@@ -66,18 +69,28 @@ rule cat_truvari_results_all:
                       min_qual = min_qual_iGenVar),
         S2   = expand("results/caller_comparison_iGenVar_only/eval/S2/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
+        S3   = expand("results/caller_comparison_iGenVar_only/eval/S3/min_qual_{min_qual}/pr_rec.txt",
+                      min_qual = min_qual_iGenVar),
+        # S4   = expand("results/caller_comparison_iGenVar_only/eval/S4/min_qual_{min_qual}/pr_rec.txt",
+        #               min_qual = min_qual_iGenVar),
         S1L1 = expand("results/caller_comparison_iGenVar_only/eval/S1L1/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
         S2L1 = expand("results/caller_comparison_iGenVar_only/eval/S2L1/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
+        S3L1 = expand("results/caller_comparison_iGenVar_only/eval/S3L1/min_qual_{min_qual}/pr_rec.txt",
+                      min_qual = min_qual_iGenVar),
         S1L2 = expand("results/caller_comparison_iGenVar_only/eval/S1L2/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
         S2L2 = expand("results/caller_comparison_iGenVar_only/eval/S2L2/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
+        S3L2 = expand("results/caller_comparison_iGenVar_only/eval/S3L2/min_qual_{min_qual}/pr_rec.txt",
+                      min_qual = min_qual_iGenVar),
         S1L3 = expand("results/caller_comparison_iGenVar_only/eval/S1L3/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
         S2L3 = expand("results/caller_comparison_iGenVar_only/eval/S2L3/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
+        S3L3 = expand("results/caller_comparison_iGenVar_only/eval/S3L3/min_qual_{min_qual}/pr_rec.txt",
+                      min_qual = min_qual_iGenVar),
         L1   = expand("results/caller_comparison_iGenVar_only/eval/L1/min_qual_{min_qual}/pr_rec.txt",
                       min_qual = min_qual_iGenVar),
         L2   = expand("results/caller_comparison_iGenVar_only/eval/L2/min_qual_{min_qual}/pr_rec.txt",
@@ -87,12 +100,17 @@ rule cat_truvari_results_all:
     output:
         S1   = temp("results/caller_comparison_iGenVar_only/eval/S1.all_results.txt"),
         S2   = temp("results/caller_comparison_iGenVar_only/eval/S2.all_results.txt"),
+        S3   = temp("results/caller_comparison_iGenVar_only/eval/S3.all_results.txt"),
+        # S4   = temp("results/caller_comparison_iGenVar_only/eval/S4.all_results.txt"),
         S1L1 = temp("results/caller_comparison_iGenVar_only/eval/S1L1.all_results.txt"),
         S2L1 = temp("results/caller_comparison_iGenVar_only/eval/S2L1.all_results.txt"),
+        S3L1 = temp("results/caller_comparison_iGenVar_only/eval/S3L1.all_results.txt"),
         S1L2 = temp("results/caller_comparison_iGenVar_only/eval/S1L2.all_results.txt"),
         S2L2 = temp("results/caller_comparison_iGenVar_only/eval/S2L2.all_results.txt"),
+        S3L2 = temp("results/caller_comparison_iGenVar_only/eval/S3L2.all_results.txt"),
         S1L3 = temp("results/caller_comparison_iGenVar_only/eval/S1L3.all_results.txt"),
         S2L3 = temp("results/caller_comparison_iGenVar_only/eval/S2L3.all_results.txt"),
+        S3L3 = temp("results/caller_comparison_iGenVar_only/eval/S3L3.all_results.txt"),
         L1   = temp("results/caller_comparison_iGenVar_only/eval/L1.all_results.txt"),
         L2   = temp("results/caller_comparison_iGenVar_only/eval/L2.all_results.txt"),
         L3   = temp("results/caller_comparison_iGenVar_only/eval/L3.all_results.txt"),
@@ -101,17 +119,31 @@ rule cat_truvari_results_all:
     run:
         shell("cat {input.S1} > {output.S1}")
         shell("cat {input.S2} > {output.S2}")
+        shell("cat {input.S3} > {output.S3}")
+        # shell("cat {input.S4} > {output.S4}")
         shell("cat {input.S1L1} > {output.S1L1}")
         shell("cat {input.S2L1} > {output.S2L1}")
+        shell("cat {input.S3L1} > {output.S3L1}")
         shell("cat {input.S1L2} > {output.S1L2}")
         shell("cat {input.S2L2} > {output.S2L2}")
+        shell("cat {input.S3L2} > {output.S3L2}")
         shell("cat {input.S1L3} > {output.S1L3}")
         shell("cat {input.S2L3} > {output.S2L3}")
+        shell("cat {input.S3L3} > {output.S3L3}")
         shell("cat {input.L1} > {output.L1}")
         shell("cat {input.L2} > {output.L2}")
         shell("cat {input.L3} > {output.L3}")
         shell("""
-            cat {output.S1} {output.S2} {output.S1L1} {output.S2L1} \
-                {output.S1L2} {output.S2L2} {output.S1L3} {output.S2L3} \
+            cat {output.S1} {output.S2} {output.S3} \
+                {output.S1L1} {output.S2L1} \
+                {output.S1L2} {output.S2L2} \
+                {output.S1L3} {output.S2L3} \
                 {output.L1} {output.L2} {output.L3} > {output.all}
         """)
+        # shell("""
+        #     cat {output.S1} {output.S2} {output.S3} {output.S4} \
+        #         {output.S1L1} {output.S2L1} \
+        #         {output.S1L2} {output.S2L2} \
+        #         {output.S1L3} {output.S2L3} \
+        #         {output.L1} {output.L2} {output.L3} > {output.all}
+        # """)
diff --git a/test/benchmark/caller_comparison_iGenVar_only/workflow/scripts/plot_all_results.R b/test/benchmark/caller_comparison_iGenVar_only/workflow/scripts/plot_all_results.R
index 7175f6db..0de5ee7a 100644
--- a/test/benchmark/caller_comparison_iGenVar_only/workflow/scripts/plot_all_results.R
+++ b/test/benchmark/caller_comparison_iGenVar_only/workflow/scripts/plot_all_results.R
@@ -22,9 +22,10 @@ f1 <- add_column(f1, min_qual = NA, .after="input_combination")
 # Combine res & f1
 total <- rbind(res, f1)
 total$input_combination = factor(total$input_combination,
-                                 levels=c('S1', 'S2', 'S1L1', 'S2L1', 'S1L2', 'S2L2', 'S1L3', 'S2L3', 'L1', 'L2', 'L3',
+                                 levels=c('S1', 'S2', 'S3', #'S4',
+                                          'S1L1', 'S2L1', 'S1L2', 'S2L2', 'S1L3', 'S2L3', 'L1', 'L2', 'L3',
                                           '0.1', '0.2', '0.3', '0.4', '0.5', '0.6', '0.7', '0.8', '0.9'),
-                                 labels=c('Illumina Paired End', 'Illumina Mate Pair',
+                                 labels=c('Illumina Paired End', 'Illumina Mate Pair', 'Illumina HiSeq', #'NA12878 WGS GRCh38',
                                           'Illumina Paired End & MtSinai PacBio', 'Illumina Mate Pair & MtSinai PacBio',
                                           'Illumina Paired End & PacBio CCS', 'Illumina Mate Pair & PacBio CCS',
                                           'Illumina Paired End & 10X Genomics', 'Illumina Mate Pair & 10X Genomics',
@@ -36,12 +37,12 @@ scale_custom <- list(
       scale_shape_manual(values = c(15, 15, 16, 16, 16, 16, 16, 16, 17, 17, 17,
                                     46, 46, 46, 46, 46, 46, 46, 46, 46)),
       # https://www.farb-tabelle.de/de/farbtabelle.htm
-      scale_color_manual(breaks = c('Illumina Paired End', 'Illumina Mate Pair',
+      scale_color_manual(breaks = c('Illumina Paired End', 'Illumina Mate Pair', 'Illumina HiSeq', 'NA12878 WGS GRCh38',
                                     'Illumina Paired End & MtSinai PacBio', 'Illumina Mate Pair & MtSinai PacBio',
                                     'Illumina Paired End & PacBio CCS', 'Illumina Mate Pair & PacBio CCS',
                                     'Illumina Paired End & 10X Genomics', 'Illumina Mate Pair & 10X Genomics',
                                     'MtSinai PacBio', 'PacBio CCS', '10X Genomics'),
-                         values = c("chartreuse3", "chartreuse1",
+                         values = c("chartreuse4", "chartreuse3", "chartreuse1", #"green3",
                                     "deepskyblue", "dodgerblue1", "dodgerblue2", "dodgerblue3", "dodgerblue4", "darkblue",
                                     "firebrick1", "firebrick3", "firebrick4",
                                     "tan", "tan", "tan", "tan", "tan", "tan", "tan", "tan", "tan"),
diff --git a/test/benchmark/caller_comparison_long_read/workflow/rules/callers.smk b/test/benchmark/caller_comparison_long_read/workflow/rules/callers.smk
index 51c863ba..21731e49 100644
--- a/test/benchmark/caller_comparison_long_read/workflow/rules/callers.smk
+++ b/test/benchmark/caller_comparison_long_read/workflow/rules/callers.smk
@@ -1,4 +1,4 @@
-sample = config["parameters"]["sample"],
+sample = config["parameters"]["sample_HG002"],
 min_var_length = config["parameters"]["min_var_length"],
 max_var_length = config["parameters"]["max_var_length"]
 
diff --git a/test/benchmark/caller_comparison_long_read/workflow/rules/eval.smk b/test/benchmark/caller_comparison_long_read/workflow/rules/eval.smk
index 1fafefea..e0a43763 100644
--- a/test/benchmark/caller_comparison_long_read/workflow/rules/eval.smk
+++ b/test/benchmark/caller_comparison_long_read/workflow/rules/eval.smk
@@ -46,14 +46,14 @@ rule truvari:
         output_dir = "results/caller_comparison_long_read/{dataset}/eval/{caller}/min_qual_{min_qual}"
     run:
         if wildcards.dataset == 'MtSinai_PacBio':
-            truth_set_gz = config["truth_set"]["gz"],
-            truth_set_bed = config["truth_set"]["bed"]
+            truth_set_gz = config["truth_set_HG002"]["gz"],
+            truth_set_bed = config["truth_set_HG002"]["bed"]
         elif wildcards.dataset == 'PacBio_CCS':
-            truth_set_gz = config["truth_set"]["gz"],
-            truth_set_bed = config["truth_set"]["bed"]
+            truth_set_gz = config["truth_set_HG002"]["gz"],
+            truth_set_bed = config["truth_set_HG002"]["bed"]
         else: # wildcards.dataset == '10X_Genomics'
-            truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-            truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+            truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+            truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
         shell("""
             rm -rf {params.output_dir} && truvari bench -b {truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
                 --passonly --includebed {truth_set_bed} &>> {log}
diff --git a/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/callers.smk b/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/callers.smk
index 8b0b73a0..ef2b4c89 100644
--- a/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/callers.smk
+++ b/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/callers.smk
@@ -1,4 +1,5 @@
-sample = config["parameters"]["sample"],
+sample = config["parameters"]["sample_HG002"],
+sample_NA12878 = config["parameters"]["sample_NA12878"],
 min_var_length = config["parameters"]["min_var_length"],
 max_var_length = config["parameters"]["max_var_length"]
 
diff --git a/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.DUP_as_INS.smk b/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.DUP_as_INS.smk
index b7daa93e..55103426 100644
--- a/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.DUP_as_INS.smk
+++ b/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.DUP_as_INS.smk
@@ -30,8 +30,8 @@ rule DUP_as_INS_truvari:
         "logs/truvari/truvari_output.{dataset}.{long_read_enhancement}.{min_qual}.log"
     params:
         output_dir = "results/caller_comparison_long_read_enhancement/{dataset}/eval/{long_read_enhancement}/DUP_as_INS.min_qual_{min_qual}",
-        truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-        truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+        truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+        truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
     shell:
         """
         rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
diff --git a/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.smk b/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.smk
index 0cbb138e..65771977 100644
--- a/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.smk
+++ b/test/benchmark/caller_comparison_long_read_enhancement/workflow/rules/eval.smk
@@ -38,8 +38,8 @@ rule truvari:
         "logs/truvari/truvari_output.{dataset}.{long_read_enhancement}.{min_qual}.log"
     params:
         output_dir = "results/caller_comparison_long_read_enhancement/{dataset}/eval/{long_read_enhancement}/min_qual_{min_qual}",
-        truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-        truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+        truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+        truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
     shell:
         """
         rm -rf {params.output_dir} && truvari bench -b {params.truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
diff --git a/test/benchmark/caller_comparison_short_read/workflow/rules/callers.smk b/test/benchmark/caller_comparison_short_read/workflow/rules/callers.smk
index 290730cc..1ef0f856 100644
--- a/test/benchmark/caller_comparison_short_read/workflow/rules/callers.smk
+++ b/test/benchmark/caller_comparison_short_read/workflow/rules/callers.smk
@@ -1,4 +1,5 @@
-sample = config["parameters"]["sample"],
+sample = config["parameters"]["sample_HG002"],
+sample_NA12878 = config["parameters"]["sample_NA12878"],
 min_var_length = config["parameters"]["min_var_length"],
 max_var_length = config["parameters"]["max_var_length"]
 
diff --git a/test/benchmark/caller_comparison_short_read/workflow/rules/eval.smk b/test/benchmark/caller_comparison_short_read/workflow/rules/eval.smk
index 1e3e0b57..445fcbf3 100644
--- a/test/benchmark/caller_comparison_short_read/workflow/rules/eval.smk
+++ b/test/benchmark/caller_comparison_short_read/workflow/rules/eval.smk
@@ -71,14 +71,14 @@ rule truvari:
         elif (wildcards.dataset == 'hg38_Sim_SNPandSV'):
             truth_set_gz = config["truth_set_simulation_SNPandSV"]["gz"]
         elif (wildcards.caller == 'GRIDSS'):
-            truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-            truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+            truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+            truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
         elif wildcards.dataset == 'Illumina_Paired_End':
-            truth_set_gz = config["truth_set"]["gz"],
-            truth_set_bed = config["truth_set"]["bed"]
+            truth_set_gz = config["truth_set_HG002"]["gz"],
+            truth_set_bed = config["truth_set_HG002"]["bed"]
         else: # wildcards.dataset == 'Illumina_Mate_Pair'
-            truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-            truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+            truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+            truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
         if (wildcards.dataset == 'Illumina_Paired_End') | (wildcards.dataset == 'Illumina_Mate_Pair'):
             shell("""
                 rm -rf {params.output_dir} && truvari bench -b {truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
diff --git a/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/callers.smk b/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/callers.smk
index 4ae948cd..79f8f0fc 100644
--- a/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/callers.smk
+++ b/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/callers.smk
@@ -1,4 +1,5 @@
-sample = config["parameters"]["sample"],
+sample = config["parameters"]["sample_HG002"],
+sample_NA12878 = config["parameters"]["sample_NA12878"],
 min_var_length = config["parameters"]["min_var_length"]
 
 rule run_Vaquita_LR:
diff --git a/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.DUP_as_INS.smk b/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.DUP_as_INS.smk
index 6c684d5c..ea694478 100644
--- a/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.DUP_as_INS.smk
+++ b/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.DUP_as_INS.smk
@@ -33,11 +33,11 @@ rule DUP_as_INS_truvari:
         output_dir = "results/caller_comparison_vaquita_lr/eval/{input_combination}/DUP_as_INS.min_qual_{min_qual}"
     run:
         if (wildcards.input_combination == 'S2') | (wildcards.input_combination == 'L3') | (wildcards.input_combination == 'S2L3'):
-            truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-            truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+            truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+            truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
         else: # S1, L1, L2, S1L1, S1L2
-            truth_set_gz = config["truth_set"]["gz"],
-            truth_set_bed = config["truth_set"]["bed"]
+            truth_set_gz = config["truth_set_HG002"]["gz"],
+            truth_set_bed = config["truth_set_HG002"]["bed"]
         shell("""
         rm -rf {params.output_dir} && truvari bench -b {truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
             --passonly --includebed {truth_set_bed} &>> {log}
diff --git a/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.smk b/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.smk
index 3cdbbb8f..46b33c40 100644
--- a/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.smk
+++ b/test/benchmark/caller_comparison_vaquita_lr/workflow/rules/eval.smk
@@ -40,11 +40,11 @@ rule truvari:
         output_dir = "results/caller_comparison_vaquita_lr/eval/{input_combination}/min_qual_{min_qual}"
     run:
         if (wildcards.input_combination == 'S2') | (wildcards.input_combination == 'L3') | (wildcards.input_combination == 'S2L3'):
-            truth_set_gz = config["truth_set_DEL_renamed_chr"]["gz"],
-            truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+            truth_set_gz = config["truth_set_HG002_DEL_renamed_chr"]["gz"],
+            truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
         else: # S1, L1, L2, S1L1, S1L2
-            truth_set_gz = config["truth_set_DEL"]["gz"],
-            truth_set_bed = config["truth_set"]["bed"]
+            truth_set_gz = config["truth_set_HG002_DEL"]["gz"],
+            truth_set_bed = config["truth_set_HG002"]["bed"]
         shell("""
         rm -rf {params.output_dir} && truvari bench -b {truth_set_gz} -c {input.vcf} -o {params.output_dir} -p 0 \
             --passonly --includebed {truth_set_bed} &>> {log}
diff --git a/test/benchmark/config/caller_comparison_config.yaml b/test/benchmark/config/caller_comparison_config.yaml
index 04d5643f..24b4d8ca 100644
--- a/test/benchmark/config/caller_comparison_config.yaml
+++ b/test/benchmark/config/caller_comparison_config.yaml
@@ -3,15 +3,18 @@
 ## NIST Stanford Illumina 6kb Mate Pair
 ### GRCh37
 short_read_bam:
-    s1: data/short_reads/GRCh37/HG002.hs37d5.2x250.sorted.bam # ~40-50x coverage (Average = 65.8713)
-    s2: data/short_reads/GRCh37/HG002.mate_pair.sorted.bam # 13-17x coverage (Average = 14.1621)
+    s1: data/short_reads/GRCh37/HG002/HG002.hs37d5.2x250.sorted.bam # ~40-50x coverage (Average = 65.8713)
+    s2: data/short_reads/GRCh37/HG002/HG002.mate_pair.sorted.bam # 13-17x coverage (Average = 14.1621)
+    s3: data/short_reads/GRCh37/HG002/HG002.hs37d5.60x.1.sorted.bam # 60x coverage (Average = 59.0516)
 ### GRCh38
-# short_read_bam:
 #     s1: data/short_reads/GRCh38/HG002.GRCh38.2x250.sorted.bam
 #     s2: data/short_reads/GRCh38/HG002.sorted.bam
+    s4: data/short_reads/GRCh38/NA12878/NA12878_S1.bam # 50x coverage (Average = 47.6849)
 short_bam_name:
     s1: "AshkenazimTrio - HG002 NA24385 Son - NIST Illumina 2x250bps Paired-end"
     s2: "AshkenazimTrio - HG002 NA24385 Son - NIST Stanford Illumina 6kb Mate Pair"
+    s3: "AshkenazimTrio - HG002 NA24385 Son - ..."
+    s4: "NA12878 - ..."
 
 # long read data
 ## MtSinai PacBio (minimap2)
@@ -64,7 +67,8 @@ simulated_short_bam_name:
 ### GRCh37
 reference_fa:
     Illumina_Paired_End: data/reference/GRCh37/hs37d5.fa
-    Illumina_Mate_Pair: data/reference/GRCh37/hg19.reordered.short.fa
+    Illumina_Mate_Pair: data/reference/GRCh37/hg19.reordered.fa
+    Illumina_HiSeq: data/reference/GRCh37/hs37d5.fa
     MtSinai_PacBio: data/reference/GRCh37/hs37d5.fa
     PacBio_CCS: data/reference/GRCh37/hs37d5.fa
     10X_Genomics: data/reference/GRCh37/hg19.reordered.fa
@@ -72,23 +76,24 @@ reference_fa:
 #     Illumina_Paired_End: data/reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa
 #     Illumina_Mate_Pair: data/reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa
 #     MtSinai_PacBio: data/reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
+    NA12878_WGS_GRCh38: data/reference/GRCh38/hg38.fa
 #     PacBio_CCS: data/reference/GRCh38/???
 #     10X_Genomics: data/reference/GRCh38/???
     simulation_ref: data/simulation_GRCh38/hg38_chr21.fa
 
-truth_set:
+truth_set_HG002:
     gz: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.vcf.gz
     bed: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.bed
-truth_set_renamed_chr:
+truth_set_HG002_renamed_chr:
     gz: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.renamed_chr.vcf.gz
     bed: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.renamed_chr.bed
-truth_set_INS:
+truth_set_HG002_INS:
     gz: data/truth_set/HG002/INS/HG002_SVs_Tier1_v0.6.INS.vcf.gz
-truth_set_INS_renamed_chr:
+truth_set_HG002_INS_renamed_chr:
     gz: data/truth_set/HG002/INS/HG002_SVs_Tier1_v0.6.INS.renamed_chr.vcf.gz
-truth_set_DEL:
+truth_set_HG002_DEL:
     gz: data/truth_set/HG002/DEL/HG002_SVs_Tier1_v0.6.DEL.vcf.gz
-truth_set_DEL_renamed_chr:
+truth_set_HG002_DEL_renamed_chr:
     gz: data/truth_set/HG002/DEL/HG002_SVs_Tier1_v0.6.DEL.renamed_chr.vcf.gz
 truth_set_simulation_default:
     gz: data/simulation_GRCh38/hg38_SV_simulation_default_sorted_fixed.vcf.gz
@@ -99,17 +104,21 @@ truth_set_simulation_noSNP:
 truth_set_simulation_SNPandSV:
     gz: data/simulation_GRCh38/hg38_SV_simulation_SNPandSV_sorted_fixed.vcf.gz
 # truth_set:
-#     gz: data/truth_set/HG002_SVs_Tier1_v0.6.Hg38.vcf.gz
-#     bed: data/truth_set/HG002_SVs_Tier1_v0.6.Hg38.bed
+#     gz: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.Hg38.vcf.gz
+#     bed: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.Hg38.bed
 # truth_set_renamed_chr:
-#     gz: data/truth_set/HG002_SVs_Tier1_v0.6.Hg38.renamed_chr.vcf.gz
-#     bed: data/truth_set/HG002_SVs_Tier1_v0.6.Hg38.renamed_chr.bed
+#     gz: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.Hg38.renamed_chr.vcf.gz
+#     bed: data/truth_set/HG002/HG002_SVs_Tier1_v0.6.Hg38.renamed_chr.bed
+truth_set_NA12878:
+    gz: data/truth_set/NA12878/NA12878_S1.vcf.gz
+    bed: data/truth_set/NA12878/NA12878_S1.ROH.bed
 
 # GRIDSS: for hg38 (UCSC chr notation)
 # blacklist: data/blacklist/ENCFF356LFX.bed
 
 parameters:
-    sample: HG002
+    sample_HG002: HG002
+    sample_NA12878: NA12878
     min_var_length: 40
     max_var_length: 1000000
 
diff --git a/test/benchmark/dataset_downloads.sh b/test/benchmark/dataset_downloads.sh
index 4d0f66ab..977f0b56 100644
--- a/test/benchmark/dataset_downloads.sh
+++ b/test/benchmark/dataset_downloads.sh
@@ -9,13 +9,15 @@ mkdir -p short_reads && cd short_reads
 
 # HG002 - NA24385:
 mkdir -p GRCh37 && cd GRCh37
+mkdir -p HG002 && cd HG002
 ## NIST Illumina 2x250bps Paired-end
 ### reference: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
 ### README: .../NIST_Illumina_2x250bps/novoalign_bams/README_update_feb2019
 ### coverage: ~40-50x (samtools depth average = 65.8713)
 ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Illumina_2x250bps/novoalign_bams/HG002.hs37d5.2x250.bam
 ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Illumina_2x250bps/novoalign_bams/HG002.hs37d5.2x250.bam.bai
-cd .. && mkdir -p GRCh38 && cd GRCh38
+cd ../.. && mkdir -p GRCh38 && cd GRCh38
+mkdir -p HG002 && cd HG002
 ### reference: GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna
 ### README: .../NIST_Illumina_2x250bps/novoalign_bams/README_update_feb2019
 ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Illumina_2x250bps/novoalign_bams/HG002.GRCh38.2x250.bam
@@ -24,19 +26,42 @@ ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Illumina_2x250bps/novoalign_ba
 ## NIST Stanford Illumina 6kb matepair
 ### Reads were then mapped to the hg19 reference genome from ucsc or the GRCh38 reference genome with decoy but no alts
 ### using bwa mem (Li 2013) with default settings, and duplicates were marked using samblaster (Faust 2014).
-cd .. && cd GRCh37
+cd ../.. && cd GRCh37/HG002
 ### reference: hg19 from ucsc
 ### README: .../NIST_Stanford_Illumina_6kb_matepair/README.NIST_Stanford_Illumina_6kb_matepair
 ### coverage: 13-17x (samtools depth average = 14.1621)
 ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Stanford_Illumina_6kb_matepair/bams/HG002.mate_pair.sorted.bam
 ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Stanford_Illumina_6kb_matepair/bams/HG002.mate_pair.sorted.bam.bai
-cd .. && cd GRCh38
+cd ../.. && cd GRCh38/HG002
 ### reference: GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna
 ### README: .../NIST_Stanford_Illumina_6kb_matepair/README.NIST_Stanford_Illumina_6kb_matepair
 ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Stanford_Illumina_6kb_matepair/bams/GRCh38/HG002.sorted.bam
 ${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_Stanford_Illumina_6kb_matepair/bams/GRCh38/HG002.sorted.bam.bai
 
-cd ../..
+## NIST HiSeq - NHGRI Illumina 300X
+cd ../.. && cd GRCh37/HG002
+### README: .../NIST_HiSeq_HG002_Homogeneity-10953946/README_NIST_Illumina_pairedend_HG002.txt
+### coverage: 60x (samtools depth average = 59.0516)
+${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.hs37d5.60x.1.bam
+${WGET} ${NCBI}/${ReferenceSamples}/${HG002}/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.hs37d5.60x.1.bam.bai
+cd ../.. && cd GRCh38/HG002
+### README: .../NIST_HiSeq_HG002_Homogeneity-10953946/README_NIST_Illumina_pairedend_HG002.txt
+${WGET} ${NCBI}/${ReferenceSamples}/${HG002}NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.GRCh38.60x.1.bam
+${WGET} ${NCBI}/${ReferenceSamples}/${HG002}NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.GRCh38.60x.1.bam.bai
+
+cd ..
+
+mkdir -p NA12878 && cd NA12878
+
+## NA12878 WGS GRCh38 - Platinum Genomes
+### Project HiSeq 2000: TruSeq PCR-Free (Platinum Genomes)
+### coverage: 50x (samtools depth average = 47.6849)
+curl 'https://basespace-data-east.s3-external-1.amazonaws.com/47c60b82082847db8cf4a7d900e530b4/NA12878_S1.bam?AWSAccessKeyId=AKIARPYQJSWQRDJKAWUT&Expires=1665567801&response-content-disposition=attachment%3Bfilename%3DNA12878_S1.bam&response-content-type=application%2Foctet-stream&Signature=ca6d7EvQOvop49gEh%2Fh6pTs2HIQ%3D' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:102.0) Gecko/20100101 Firefox/102.0' -H 'Accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,*/*;q=0.8' -H 'Accept-Language: de,en-US;q=0.7,en;q=0.3' -H 'Accept-Encoding: gzip, deflate, br' -H 'Referer: https://basespace.illumina.com/' -H 'Connection: keep-alive' -H 'Upgrade-Insecure-Requests: 1' -H 'Sec-Fetch-Dest: document' -H 'Sec-Fetch-Mode: navigate' -H 'Sec-Fetch-Site: cross-site' -H 'Sec-Fetch-User: ?1' \
+    --output NA12878_S1.bam
+curl 'https://basespace-data-east.s3-external-1.amazonaws.com/47c60b82082847db8cf4a7d900e530b4/NA12878_S1.bam.bai?AWSAccessKeyId=AKIARPYQJSWQRDJKAWUT&Expires=1665568255&response-content-disposition=attachment%3Bfilename%3DNA12878_S1.bam.bai&response-content-type=application%2Foctet-stream&Signature=PQNrr3brzcLKkqZRgh1zw3AJcuM%3D' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:102.0) Gecko/20100101 Firefox/102.0' -H 'Accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,*/*;q=0.8' -H 'Accept-Language: de,en-US;q=0.7,en;q=0.3' -H 'Accept-Encoding: gzip, deflate, br' -H 'Referer: https://basespace.illumina.com/' -H 'Connection: keep-alive' -H 'Upgrade-Insecure-Requests: 1' -H 'Sec-Fetch-Dest: document' -H 'Sec-Fetch-Mode: navigate' -H 'Sec-Fetch-Site: cross-site' -H 'Sec-Fetch-User: ?1' \
+--output NA12878_S1.bam.bai
+
+cd ../../..
 
 echo "$(tput setaf 1)$(tput setab 7)------- short reads downloaded (3.1/3.4) --------$(tput sgr 0)" 1>&3
 
@@ -120,6 +145,7 @@ echo "$(tput setaf 1)$(tput setab 7)------- reference downloaded (3.3/3.4) -----
 
 # -------- -------- get truth set ../../data -------- -------- #
 mkdir -p truth_set && cd truth_set
+mkdir -p HG002 && cd HG002
 
 # HG002 - NA24385:
 ## GRCh37
@@ -131,10 +157,22 @@ ${WGET} ${NCBI}/${ReferenceSamples}/AshkenazimTrio/analysis/NIST_SVs_Integration
 # ${WGET} ${NCBI}/${ReferenceSamples}/AshkenazimTrio/analysis/10XGenomics_ChromiumGenome_LongRanger2.2_Supernova2.0.1_04122018/GRCh38/NA24385_300G/NA24385.GRCh38.large_svs.vcf.gz
 # ${WGET} ${NCBI}/${ReferenceSamples}/AshkenazimTrio/analysis/10XGenomics_ChromiumGenome_LongRanger2.2_Supernova2.0.1_04122018/GRCh38/NA24385_300G/NA24385.GRCh38.large_svs.vcf.gz.tbi
 
+cd ..
+mkdir -p NA12878 && cd NA12878
+
+## NA12878 WGS GRCh38 - Platinum Genomes
+### Project HiSeq 2000: TruSeq PCR-Free (Platinum Genomes)
+curl 'https://basespace-data-east.s3-external-1.amazonaws.com/47c60b82082847db8cf4a7d900e530b4/NA12878_S1.vcf.gz?AWSAccessKeyId=AKIARPYQJSWQRDJKAWUT&Expires=1665568301&response-content-disposition=attachment%3Bfilename%3DNA12878_S1.vcf.gz&response-content-type=application%2Fx-gzip&Signature=yF%2Fk2li9bNaCdbQxqoX0BKtIdww%3D' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:102.0) Gecko/20100101 Firefox/102.0' -H 'Accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,*/*;q=0.8' -H 'Accept-Language: de,en-US;q=0.7,en;q=0.3' -H 'Accept-Encoding: gzip, deflate, br' -H 'Referer: https://basespace.illumina.com/' -H 'Connection: keep-alive' -H 'Upgrade-Insecure-Requests: 1' -H 'Sec-Fetch-Dest: document' -H 'Sec-Fetch-Mode: navigate' -H 'Sec-Fetch-Site: cross-site' -H 'Sec-Fetch-User: ?1' \
+--output NA12878_S1.vcf.gz
+curl 'https://basespace-data-east.s3-external-1.amazonaws.com/47c60b82082847db8cf4a7d900e530b4/NA12878_S1.vcf.gz.tbi?AWSAccessKeyId=AKIARPYQJSWQRDJKAWUT&Expires=1665568395&response-content-disposition=attachment%3Bfilename%3DNA12878_S1.vcf.gz.tbi&response-content-type=application%2Foctet-stream&Signature=nS2QjrLPMsvAgJFWn%2BHjmXfTdWw%3D' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:102.0) Gecko/20100101 Firefox/102.0' -H 'Accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,*/*;q=0.8' -H 'Accept-Language: de,en-US;q=0.7,en;q=0.3' -H 'Accept-Encoding: gzip, deflate, br' -H 'Referer: https://basespace.illumina.com/' -H 'Connection: keep-alive' -H 'Upgrade-Insecure-Requests: 1' -H 'Sec-Fetch-Dest: document' -H 'Sec-Fetch-Mode: navigate' -H 'Sec-Fetch-Site: cross-site' -H 'Sec-Fetch-User: ?1' \
+--output NA12878_S1.vcf.gz.tbi
+curl 'https://basespace-data-east.s3-external-1.amazonaws.com/47c60b82082847db8cf4a7d900e530b4/NA12878_S1.ROH.bed?AWSAccessKeyId=AKIARPYQJSWQRDJKAWUT&Expires=1665568438&response-content-disposition=attachment%3Bfilename%3DNA12878_S1.ROH.bed&response-content-type=application%2Foctet-stream&Signature=yijtINIcFla%2FLMGZPCKLospTIWI%3D' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.15; rv:102.0) Gecko/20100101 Firefox/102.0' -H 'Accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,*/*;q=0.8' -H 'Accept-Language: de,en-US;q=0.7,en;q=0.3' -H 'Accept-Encoding: gzip, deflate, br' -H 'Referer: https://basespace.illumina.com/' -H 'Connection: keep-alive' -H 'Upgrade-Insecure-Requests: 1' -H 'Sec-Fetch-Dest: document' -H 'Sec-Fetch-Mode: navigate' -H 'Sec-Fetch-Site: cross-site' -H 'Sec-Fetch-User: ?1' \
+--output NA12878_S1.ROH.bed
+
 # HG005 - NA24631: (there is no truth set so far)
 # ${WGET} ${NCBI}/${ReferenceSamples}/...     .vcf.gz
 # ${WGET} ${NCBI}/${ReferenceSamples}/...     .vcf.gz.tbi
 # ${WGET} ${NCBI}/${ReferenceSamples}/...     .bed
 
-cd ..
+cd ../..
 echo "$(tput setaf 1)$(tput setab 7)------- truth set downloaded (3.4/3.4) --------$(tput sgr 0)" 1>&3
diff --git a/test/benchmark/parameter_benchmarks/Snakefile b/test/benchmark/parameter_benchmarks/Snakefile
index 9d386d58..aa31596f 100644
--- a/test/benchmark/parameter_benchmarks/Snakefile
+++ b/test/benchmark/parameter_benchmarks/Snakefile
@@ -96,8 +96,8 @@ rule truvari:
         summary = "results/parameter_benchmarks/{dataset}/truvari/{parameter_name}/{parameter_value}_min_qual_{min_qual}/summary.txt"
     params:
         output_dir = "results/parameter_benchmarks/{dataset}/truvari/{parameter_name}/{parameter_value}_min_qual_{min_qual}",
-        truth_set_gz = config["truth_set_renamed_chr"]["gz"],
-        truth_set_bed = config["truth_set_renamed_chr"]["bed"]
+        truth_set_gz = config["truth_set_HG002_renamed_chr"]["gz"],
+        truth_set_bed = config["truth_set_HG002_renamed_chr"]["bed"]
     log:
         "logs/parameter_benchmarks/truvari/{dataset}/{parameter_name}_{parameter_value}_min_qual_{min_qual}_output.log"
     run:
diff --git a/test/benchmark/prepare_BAM_with_crossmap.sh b/test/benchmark/prepare_BAM_with_crossmap.sh
index b216acb4..e2c69043 100644
--- a/test/benchmark/prepare_BAM_with_crossmap.sh
+++ b/test/benchmark/prepare_BAM_with_crossmap.sh
@@ -26,17 +26,21 @@ less data/reference/GRCh37/hg19.reordered.fa | sed -e '/>chr_1/,$d' >> data/refe
 echo "$(tput setaf 1)$(tput setab 7)------- reference files prepared (5.2/9.6) --------$(tput sgr 0)" 1>&3
 
 # Illumina Paired End
-samtools sort short_reads/GRCh37/HG002.hs37d5.2x250.bam -o short_reads/GRCh37/HG002.hs37d5.2x250.sorted.bam
-samtools sort short_reads/GRCh38/HG002.GRCh38.2x250.bam -o short_reads/GRCh38/HG002.GRCh38.2x250.sorted.bam
-samtools index short_reads/GRCh37/HG002.hs37d5.2x250.sorted.bam
-samtools index short_reads/GRCh38/HG002.GRCh38.2x250.sorted.bam
+samtools sort short_reads/GRCh37/HG002/HG002.hs37d5.2x250.bam -o short_reads/GRCh37/HG002/HG002.hs37d5.2x250.sorted.bam
+samtools sort short_reads/GRCh38/HG002/HG002.GRCh38.2x250.bam -o short_reads/GRCh38/HG002/HG002.GRCh38.2x250.sorted.bam
+samtools index short_reads/GRCh37/HG002/HG002.hs37d5.2x250.sorted.bam
+samtools index short_reads/GRCh38/HG002/HG002.GRCh38.2x250.sorted.bam
+
+# Illumina HiSeq
+samtools sort data/short_reads/GRCh37/HG002/HG002.hs37d5.60x.1.bam -o data/short_reads/GRCh37/HG002/HG002.hs37d5.60x.1.sorted.bam
+samtools index data/short_reads/GRCh37/HG002/HG002.hs37d5.60x.1.sorted.bam
 
 # MtSinai PacBio
 ## Add MD tag for Sniffles
-samtools calmd --threads 16 -Q -b long_reads/GRCh37/HG002_PacBio_GRCh37.bam \
-    > long_reads/GRCh37/HG002_PacBio_GRCh37.md.bam reference/GRCh37/hs37d5.fa
-samtools calmd --threads 16 -Q -b long_reads/GRCh38/HG002_PacBio_GRCh38.bam \
-    > long_reads/GRCh38/HG002_PacBio_GRCh38.md.bam reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
+samtools calmd --threads 16 -Q -b long_reads/GRCh37/HG002/HG002_PacBio_GRCh37.bam \
+    > long_reads/GRCh37/HG002/HG002_PacBio_GRCh37.md.bam reference/GRCh37/hs37d5.fa
+samtools calmd --threads 16 -Q -b long_reads/GRCh38/HG002/HG002_PacBio_GRCh38.bam \
+    > long_reads/GRCh38/HG002/HG002_PacBio_GRCh38.md.bam reference/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
 
 # PacBio CCS 10kb
 ## Add MD tag for Sniffles