diff --git a/analysis-v2/phab_cm/1_phab_eval_vcfs.sh b/analysis-v2/phab_cm/1_phab_eval_vcfs.sh
index 32c16b0..1effc65 100755
--- a/analysis-v2/phab_cm/1_phab_eval_vcfs.sh
+++ b/analysis-v2/phab_cm/1_phab_eval_vcfs.sh
@@ -2,15 +2,15 @@
 
 source globals.sh
 
-# # truvari phab VCF normalization v4.0
-# source ~/software/Truvari-v4.0.0/venv3.10/bin/activate
+# # truvari phab VCF normalization v4.2.1
+# source ~/software/Truvari-4.2.1/venv3.10/bin/activate
 # mkdir -p $out/phab
 # for i in "${!query_names[@]}"; do
-#     echo "truvari v4.0: phab mafft for '${query_names[i]}'"
+#     echo "phab: mafft for '${query_names[i]}'"
 #     truvari phab \
 #         -r $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
-#         -b $data/${truth_name}-${truth_version}/split/${truth_name}.all.vcf.gz \
-#         -c $data/${query_names[i]}-${query_versions[i]}/split/${query_names[i]}.all.vcf.gz \
+#         -b $data/${truth_name}-${truth_version}/split/${truth_name}.most.vcf.gz \
+#         -c $data/${query_names[i]}-${query_versions[i]}/split/${query_names[i]}.most.vcf.gz \
 #         --bSamples HG002 \
 #         --cSamples HG002 \
 #         -f $data/refs/$ref_name \
@@ -55,55 +55,51 @@ for i in "${!query_names[@]}"; do
         $out/phab/${query_names[i]}.TRUTH.vcf.gz \
         $data/refs/$ref_name \
         --bed $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
-        -l 1000 -v 2 \
+        -l 1000 \
         -p $out/phab-vcfdist/${query_names[i]}. \
         2> $out/phab-vcfdist/${query_names[i]}.log
 done
 
-# # vcfeval evaluation
-# mkdir -p $out/phab-vcfeval
-# for i in "${!query_names[@]}"; do
-#     echo "phab-vcfeval: evaluating '${query_names[i]}'"
-#     rm -r $out/phab-vcfeval/${query_names[i]}
-#     $timer -v $rtg vcfeval \
-#         -b $out/phab/${query_names[i]}.TRUTH.vcf.gz \
-#         -c $out/phab/${query_names[i]}.QUERY.vcf.gz \
-#         -t $data/refs/${ref_name}.sdf \
-#         -m ga4gh \
-#         -e $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
-#         --threads 64 \
-#         --ref-overlap \
-#         --all-records \
-#         -o $out/phab-vcfeval/${query_names[i]} \
-#         2> $out/phab-vcfeval/${query_names[i]}.log
-#     gunzip $out/phab-vcfeval/${query_names[i]}/output.vcf.gz
-# done
-
-# awk 'BEGIN{OFS="\t"} {print $1,$2,$3-1}' \
-#     $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
-#     > $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.minus1.bed
+# vcfeval evaluation
+mkdir -p $out/phab-vcfeval
+for i in "${!query_names[@]}"; do
+    echo "phab-vcfeval: evaluating '${query_names[i]}'"
+    rm -r $out/phab-vcfeval/${query_names[i]}
+    $timer -v $rtg vcfeval \
+        -b $out/phab/${query_names[i]}.TRUTH.vcf.gz \
+        -c $out/phab/${query_names[i]}.QUERY.vcf.gz \
+        -t $data/refs/${ref_name}.sdf \
+        --bed-regions $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
+        --evaluation-regions $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
+        --threads 64 \
+        -m ga4gh \
+        --ref-overlap \
+        --all-records \
+        -o $out/phab-vcfeval/${query_names[i]} \
+        2> $out/phab-vcfeval/${query_names[i]}.log
+    gunzip $out/phab-vcfeval/${query_names[i]}/output.vcf.gz
+done
 
-# # Truvari evaluation
-# mkdir -p $out/phab-truvari
-# source ~/software/Truvari-4.1.0/venv3.10/bin/activate
-# for i in "${!query_names[@]}"; do
-#     echo "Truvari: evaluating '${query_names[i]}'"
-#     rm -r $out/phab-truvari/${query_names[i]}
-#     $timer -v truvari bench \
-#         -b $out/phab/${query_names[i]}.TRUTH.vcf.gz \
-#         -c $out/phab/${query_names[i]}.QUERY.vcf.gz \
-#         -f $data/refs/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta \
-#         --includebed $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.minus1.bed \
-#         --no-ref a \
-#         --sizemin 1 --sizefilt 1 --sizemax 1000 \
-#         --pick single \
-#         --typeignore \
-#         --dup-to-ins \
-#         -o $out/phab-truvari/${query_names[i]} \
-#         2> $out/phab-truvari/${query_names[i]}.log
-#     laytr tru2ga \
-#         -i $out/phab-truvari/${query_names[i]}/ \
-#         -o $out/phab-truvari/${query_names[i]}/result
-#     gunzip $out/phab-truvari/${query_names[i]}/result*.gz
-# done
-# deactivate
+# Truvari evaluation
+mkdir -p $out/phab-truvari
+source ~/software/Truvari-4.2.1/venv3.10/bin/activate
+for i in "${!query_names[@]}"; do
+    echo "phab-truvari: evaluating '${query_names[i]}'"
+    rm -r $out/phab-truvari/${query_names[i]}
+    $timer -v truvari bench \
+        -b $out/phab/${query_names[i]}.TRUTH.vcf.gz \
+        -c $out/phab/${query_names[i]}.QUERY.vcf.gz \
+        --includebed $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
+        --no-ref a \
+        --sizemin 1 --sizefilt 1 --sizemax 1000 \
+        --pick single \
+        --typeignore \
+        --dup-to-ins \
+        -o $out/phab-truvari/${query_names[i]} \
+        2> $out/phab-truvari/${query_names[i]}.log
+    truvari ga4gh \
+        -i $out/phab-truvari/${query_names[i]}/ \
+        -o $out/phab-truvari/${query_names[i]}/result
+    gunzip $out/phab-truvari/${query_names[i]}/result*.gz
+done
+deactivate
diff --git a/analysis-v2/phab_cm/2_eval_vcfs.sh b/analysis-v2/phab_cm/2_eval_vcfs.sh
deleted file mode 100755
index 9fd1aa5..0000000
--- a/analysis-v2/phab_cm/2_eval_vcfs.sh
+++ /dev/null
@@ -1,118 +0,0 @@
-#!/bin/bash
-
-source globals.sh
-
-# vcfdist evaluation
-mkdir -p $out/vcfdist
-for i in "${!query_names[@]}"; do
-    echo "vcfdist: evaluating '${query_names[i]}'"
-    $timer -v /home/timdunn/vcfdist/src/vcfdist \
-        $data/${query_names[i]}-${query_versions[i]}/split/${query_names[i]}.all.vcf.gz \
-        $data/${truth_name}-${truth_version}/split/${truth_name}.all.vcf.gz \
-        $data/refs/$ref_name \
-        --bed $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
-        -t 64 -r 128 \
-        -l 1000 \
-        -p $out/vcfdist/${query_names[i]}. \
-        2> $out/vcfdist/${query_names[i]}.log
-done
-
-# vcfeval evaluation
-mkdir -p $out/vcfeval
-for i in "${!query_names[@]}"; do
-    echo "vcfeval: evaluating '${query_names[i]}'"
-    rm -r $out/vcfeval/${query_names[i]}
-    $timer -v $rtg vcfeval \
-        -b $data/${truth_name}-${truth_version}/split/${truth_name}.all.vcf.gz \
-        -c $data/${query_names[i]}-${query_versions[i]}/split/${query_names[i]}.all.vcf.gz \
-        -t $data/refs/${ref_name}.sdf \
-        -e $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.bed \
-        --threads 64 \
-        --ref-overlap \
-        --vcf-score-field=QUAL \
-        -o $out/vcfeval/${query_names[i]} \
-        2> $out/vcfeval/${query_names[i]}.log
-    gunzip $out/vcfeval/${query_names[i]}/*.vcf.gz
-done
-
-source ~/software/Truvari-4.1.0/venv3.10/bin/activate
-
-# # truvari evaluation
-# mkdir -p $out/truvari
-# for i in "${!query_names[@]}"; do
-#     echo "truvari: evaluating '${query_names[i]}'"
-#     rm -r $out/truvari/${query_names[i]}
-#     $timer -v truvari bench \
-#         -b $data/${truth_name}-${truth_version}/split/${truth_name}.all.vcf.gz \
-#         -c $data/${query_names[i]}-${query_versions[i]}/split/${query_names[i]}.all.vcf.gz \
-#         -f $data/refs/$ref_name \
-#         --bSample HG002 \
-#         --cSample HG002 \
-#         --includebed $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.minus1.bed \
-#         --no-ref a \
-#         --sizemin 1 --sizefilt 1 --sizemax 1000 \
-#         --pick single \
-#         --typeignore \
-#         --dup-to-ins \
-#         -o $out/truvari/${query_names[i]} \
-#         2> $out/truvari/${query_names[i]}.log
-#     laytr tru2ga \
-#         -i $out/truvari/${query_names[i]}/ \
-#         -o $out/truvari/${query_names[i]}/result
-#     gunzip $out/truvari/${query_names[i]}/result*.gz
-# done
-
-# # wfa/mafft refine
-# for aln in "${truvari_refine_options[@]}"; do
-#     for i in "${!query_names[@]}"; do
-#         echo "\ntruvari: ${aln} refine '${query_names[i]}'"
-#         mkdir -p $out/truvari-${aln}
-#         rm -rf $out/truvari-${aln}/${query_names[i]}
-#         cp -r $out/truvari/${query_names[i]} \
-#               $out/truvari-${aln}/${query_names[i]}
-#         $timer -v truvari refine \
-#             -f $data/refs/$ref_name \
-#             -t 64 \
-#             --use-original-vcfs \
-#             --recount \
-#             --align ${aln} \
-#             $out/truvari-${aln}/${query_names[i]} \
-#             2> $out/truvari-${aln}/${query_names[i]}.log
-#         echo "laytr: ${aln} refine '${query_names[i]}'"
-#         laytr tru2ga \
-#             -i $out/truvari-${aln}/${query_names[i]}/phab_bench/ \
-#             -o $out/truvari-${aln}/${query_names[i]}/phab_bench/result
-#         gunzip $out/truvari-${aln}/${query_names[i]}/phab_bench/result*.gz
-#         rm -f $out/truvari-${aln}/${query_names[i]}/*.gz
-#         rm -f $out/truvari-${aln}/${query_names[i]}/*.vcf
-#         rm -f $out/truvari-${aln}/${query_names[i]}/*.tbi
-#         echo "bedtools: exclude phab '${query_names[i]}'"
-#         bedtools subtract \
-#             -a $data/giab-tr-v4.20/GIABTR.HG002.benchmark.chr20.minus1.bed \
-#             -b $out/truvari-${aln}/${query_names[i]}/candidate.refine.bed \
-#             > $out/truvari-${aln}/${query_names[i]}/no-refine.bed
-#         echo "truvari: bench excluded phab '${query_names[i]}'"
-#         rm -rf $out/truvari-${aln}/${query_names[i]}/no_phab_bench
-#         truvari bench \
-#             -b $data/${truth_name}-${truth_version}/split/${truth_name}.all.vcf.gz \
-#             -c $data/${query_names[i]}-${query_versions[i]}/split/${query_names[i]}.all.vcf.gz \
-#             -f $data/refs/$ref_name \
-#             --bSample HG002 \
-#             --cSample HG002 \
-#             --includebed $out/truvari-${aln}/${query_names[i]}/no-refine.bed \
-#             --no-ref a \
-#             --sizemin 1 --sizefilt 1 --sizemax 1000 \
-#             --pick single \
-#             --typeignore \
-#             --dup-to-ins \
-#             -o $out/truvari-${aln}/${query_names[i]}/no_phab_bench \
-#             2> $out/truvari-${aln}/${query_names[i]}/no_phab_bench.log
-#         echo "laytr: ${aln} refine '${query_names[i]}'"
-#         laytr tru2ga \
-#             -i $out/truvari-${aln}/${query_names[i]}/no_phab_bench/ \
-#             -o $out/truvari-${aln}/${query_names[i]}/no_phab_bench/result
-#         gunzip $out/truvari-${aln}/${query_names[i]}/no_phab_bench/result*.gz
-#     done
-# done
-
-deactivate
diff --git a/analysis-v2/phab_cm/3_gen_cm.py b/analysis-v2/phab_cm/2_gen_cm.py
similarity index 98%
rename from analysis-v2/phab_cm/3_gen_cm.py
rename to analysis-v2/phab_cm/2_gen_cm.py
index ec74d09..0e78ab1 100644
--- a/analysis-v2/phab_cm/3_gen_cm.py
+++ b/analysis-v2/phab_cm/2_gen_cm.py
@@ -160,7 +160,7 @@ def match(record1, record2):
     if var in truvari_records: (size, tv_type, gts) = truvari_records[var]
     if vd_type and ve_type and tv_type:
         counts[size][vd_type-1][(ve_type-1)*2 + tv_type-1] += gts
-    if size == SZ_SNP and vd_type and ve_type and not tv_type:
+    elif size == SZ_SNP and vd_type and ve_type and not tv_type:
         counts[size][vd_type-1][(ve_type-1)*2] += gts
 
 for size_idx in range(SZ_DIMS):
diff --git a/analysis-v2/phab_cm/3_sum_cm.py b/analysis-v2/phab_cm/3_sum_cm.py
index d0f280d..463a7d8 100644
--- a/analysis-v2/phab_cm/3_sum_cm.py
+++ b/analysis-v2/phab_cm/3_sum_cm.py
@@ -106,7 +106,7 @@ def hap2(var):
 
 
 
-am = pp = am_diff = snp = 0
+am = pp = am_diff = snps = dels = 0
 for ds in datasets:
     truvari_records = {}
     vcfdist_records = {}
@@ -166,14 +166,20 @@ def hap2(var):
         if var in vcfeval_records: (size, ve_type, ve_bk) = vcfeval_records[var]
         if var in truvari_records: (size, tv_type, tv_bk) = truvari_records[var]
         skips[0 if vd_type else 1][0 if ve_type else 1][0 if tv_type else 1] += 1
-        if vd_type and ve_type and tv_type:
+
+        loc, ref, alt, gt = var.split()
+
+        if vd_type and not ve_type and not tv_type:
+            print(f"{ds} {var} VD={cats[vd_type]}:{vd_bk}")
+
+        if vd_type and ve_type and tv_type: # all tools compare
             i = vd_type-1
             j = (ve_type-1)*2 + tv_type-1
             counts[size][i][j] += 1
             if i == 0 and j == 1:
                 if tv_bk == "am": # truvari allele match
                     am += 1
-                    print(f"{ds} {var} VD={cats[vd_type]}:{vd_bk} VE={cats[ve_type]}:{ve_bk} TV={cats[tv_type]}:{tv_bk}")
+                    # print(f"{ds} {var} VD={cats[vd_type]}:{vd_bk} VE={cats[ve_type]}:{ve_bk} TV={cats[tv_type]}:{tv_bk}")
                 else:
                     # print(f"{ds} {var} VD={cats[vd_type]}:{vd_bk} VE={cats[ve_type]}:{ve_bk} TV={cats[tv_type]}:{tv_bk}")
                     pass
@@ -201,25 +207,31 @@ def hap2(var):
 
         elif size == SZ_SNP and vd_type and ve_type and not tv_type: # Truvari skips SNPs
             counts[size][vd_type-1][(ve_type-1)*2] += 1
-            snp += 1
-        elif ve_type and tv_type and not vd_type:
+            snps += 1
+
+        elif vd_type and ve_type and not tv_type: # Truvari skip
             # print(f"{ds} {var} VD={cats[vd_type]}:{vd_bk} VE={cats[ve_type]}:{ve_bk} TV={cats[tv_type]}:{tv_bk}")
+            # if len(ref) > len(alt):
+            #     dels += 1
             pass
 
+        elif ve_type and tv_type and not vd_type:
+            print(f"{ds} {var} VD={cats[vd_type]}:{vd_bk} VE={cats[ve_type]}:{ve_bk} TV={cats[tv_type]}:{tv_bk}")
+
 
 sum_counts = counts[SZ_INDEL][:][:] + counts[SZ_SV][:][:]
 print("[truvari-only TP] more lenient allele match:", am)
 print("[vcfeval-only FP] inexact match:", pp)
 print("[vcfeval-only FP] allele match stringency diff:", am_diff)
 
-# print("         all keep:", skips[0][0][0])
-# print("         all skip:", skips[1][1][1])
-# print("vcfdist-only skip:", skips[1][0][0])
-# print("vcfeval-only skip:", skips[0][1][0])
-# print("truvari-only skip:", skips[0][0][1], f" of which {snp} are SNPs")
-# print("vcfdist-only keep:", skips[0][1][1])
-# print("vcfeval-only keep:", skips[1][0][1])
-# print("truvari-only keep:", skips[1][1][0])
+print("         all keep:", skips[0][0][0])
+print("         all skip:", skips[1][1][1])
+print("vcfdist-only skip:", skips[1][0][0])
+print("vcfeval-only skip:", skips[0][1][0])
+print("truvari-only skip:", skips[0][0][1], f" of which {snps} are SNPs and {dels} are DELs")
+print("vcfdist-only keep:", skips[0][1][1])
+print("vcfeval-only keep:", skips[1][0][1])
+print("truvari-only keep:", skips[1][1][0])
 
 fig, ax = plt.subplots(figsize=(3,6))
 ax.matshow(np.log(sum_counts + 0.1), cmap='Greys')
diff --git a/analysis-v2/phab_cm/globals.sh b/analysis-v2/phab_cm/globals.sh
index f589bc9..48a102a 100755
--- a/analysis-v2/phab_cm/globals.sh
+++ b/analysis-v2/phab_cm/globals.sh
@@ -27,8 +27,3 @@ query_versions=(
     "v4"
     "v4.20"
 )
-
-truvari_refine_options=(
-    "wfa"
-    "mafft"
-)
diff --git a/analysis-v2/phab_cm/vcfdist_truvari_compare.py b/analysis-v2/phab_cm/vcfdist_truvari_compare.py
deleted file mode 100644
index 9fe4acd..0000000
--- a/analysis-v2/phab_cm/vcfdist_truvari_compare.py
+++ /dev/null
@@ -1,241 +0,0 @@
-import vcf
-import numpy as np
-import matplotlib.pyplot as plt
-
-# chr20, with phab
-truvari_prefix = "./truvari/giab-tr/result_"
-vcfdist_prefix = "./vcfdist/giab-tr."
-do_print = False
-
-SIZE             = 0
-SZ_SNP           = 0
-SZ_INDEL_1_50    = 1
-SZ_INDEL_50_500  = 2
-SZ_INDEL_500PLUS = 3
-SZ_DIMS = 4
-sizes = ["SNP", "INDEL 1-50", "INDEL 50-500", "INDEL 500+"]
-
-VD_NONE = 0
-VD_FP   = 1
-VD_PP   = 2
-VD_TP   = 3
-VD_DIMS = 4
-vd_cats = ["None", "FP", "PP", "TP"]
-
-TV_NONE = 0
-TV_FP   = 1
-TV_PP   = 2
-TV_TP   = 3
-TV_DIMS = 4
-tv_cats = ["None", "FP", "PP", "TP"]
-
-tv_min_seq_pct = 0.7
-tv_min_size_pct = 0.7
-tv_min_ovlp_pct = 0.0
-
-counts = np.zeros((SZ_DIMS, VD_DIMS, TV_DIMS))
-
-def get_size(ref : str, alt : str):
-    if len(ref) == 1 and len(alt) == 1:
-        return SZ_SNP
-    else:
-        size_diff = abs(len(ref) - len(alt))
-        if size_diff == 0:
-            print("ERROR: size 0 INDEL")
-            exit(1)
-        elif size_diff <= 50:
-            return SZ_INDEL_1_50
-        elif size_diff <= 500:
-            return SZ_INDEL_50_500
-        else:
-            return SZ_INDEL_500PLUS
-
-def get_vd_type(credit : float):
-    if credit >= 0 and credit < 0.7:
-        return VD_FP
-    elif credit >= 0.7 and credit < 1:
-        return VD_PP
-    elif credit == 1:
-        return VD_TP
-    else:
-        print("ERROR: credit out of range")
-        exit(1)
-
-
-def get_tv_type(tv_type : str, seqsim : float):
-    if seqsim is None:
-        return TV_FP
-    if tv_type == "TP" and  seqsim < 1 and seqsim >= 0.7:
-        return TV_PP
-    if tv_type == "TP":
-        return TV_TP
-    if tv_type == "FP":
-        return TV_FP
-
-
-# for callset in ["query", "truth"]:
-for callset in ["query"]:
-
-    # parse vcfdist and truvari summary VCFs
-    vcfdist_vcf = vcf.Reader(open(f"{vcfdist_prefix}summary.vcf", "r"))
-    truvari_vcf = vcf.Reader(open(f"{truvari_prefix}{callset}.vcf", "r"))
-    name = callset.upper()
-    print(name)
-    tv_used, vd_used, vd_2used = True, True, False
-    this_ctg = "chr1"
-    print(this_ctg)
-
-    while True:
-
-        # get next valid records for each
-        if tv_used: tv_rec = next(truvari_vcf, None)
-        if vd_used: vd_rec = next(vcfdist_vcf, None)
-        if vd_2used: vd_rec = next(vcfdist_vcf, None)
-        while vd_rec != None and vd_rec.genotype(name)['BD'] == None: # skip other callset
-            vd_rec = next(vcfdist_vcf, None)
-        while tv_rec != None and tv_rec.ALT[0] == "*": # skip nested var
-            tv_rec = next(truvari_vcf, None)
-        tv_used, vd_used, vd_2used = False, False, False
-
-        if do_print:
-            print("============================================================")
-            print("Truvari:", tv_rec)
-            print("vcfdist:", vd_rec)
-
-        # we've finished iterating through both VCFs
-        if tv_rec == None and vd_rec == None: break
-
-        # we've finished this contig for both VCFs
-        if (tv_rec == None or tv_rec.CHROM != this_ctg) and \
-                (vd_rec == None or vd_rec.CHROM != this_ctg):
-            if tv_rec == None:
-                this_ctg = vd_rec.CHROM
-                print(this_ctg)
-            elif vd_rec == None:
-                this_ctg = tv_rec.CHROM
-                print(this_ctg)
-            elif tv_rec.CHROM == vd_rec.CHROM:
-                this_ctg = tv_rec.CHROM
-                print(this_ctg)
-            else:
-                print("ERROR: different contigs up next")
-
-        # if we've finished only one VCF, set high position
-        tv_pos = 2_000_000_000 if tv_rec == None else (
-                1_000_000_000 if tv_rec.CHROM != this_ctg else tv_rec.POS)
-        vd_pos = 2_000_000_000 if vd_rec == None else (
-                1_000_000_000 if vd_rec.CHROM != this_ctg else vd_rec.POS)
-
-        if tv_pos == vd_pos: # position match
-            if do_print: print(f"TV VD {name} {tv_rec.genotype(name)['GT']} {vd_rec.genotype(name)['GT']} {tv_rec.CHROM}:{tv_rec.POS}\t{tv_rec.REF}\t{tv_rec.ALT[0]}")
-            if tv_rec.REF == vd_rec.REF and tv_rec.ALT[0] == vd_rec.ALT[0]: # full match
-                tv_used, vd_used = True, True
-                if tv_rec.genotype(name)['GT'] == '1|1' or tv_rec.genotype(name)['GT'] == '1/1':
-                    vd_2used = True # skip second split of this GT
-                size = get_size(tv_rec.REF, tv_rec.ALT[0])
-                vd_type = get_vd_type(float(vd_rec.genotype(name)['BC']))
-                tv_type = get_tv_type(tv_rec.genotype(name)['BD'], tv_rec.INFO['PctSeqSimilarity'])
-                counts[size][vd_type][tv_type] += 2 if vd_2used else 1
-                if vd_type == VD_TP and tv_type == TV_FP:
-                    if do_print: print("vcfdist TP, Truvari FP")
-                if vd_type == VD_FP and tv_type == TV_TP:
-                    if do_print: print("vcfdist FP, Truvari TP")
-
-                # skip if info unavailable
-                if tv_rec.INFO['PctSeqSimilarity'] == None or \
-                        tv_rec.INFO['PctSizeSimilarity'] == None or \
-                        tv_rec.INFO['PctRecOverlap'] == None:
-                    counts[size][vd_type][TV_FP] += 1
-                    continue
-
-            # vcfdist SNP adjacent to INS
-            elif len(vd_rec.REF) == 1 and len(vd_rec.ALT[0]) == 1:
-                vd_used = True
-                size = get_size(vd_rec.REF, vd_rec.ALT[0])
-                vd_type = get_vd_type(float(vd_rec.genotype(name)['BC']))
-                tv_type = TV_NONE
-                counts[size][vd_type][tv_type] += 1
-
-            else: # position but not allele match, likely different phasing order
-
-                # get next record for each
-                tv_rec_next = next(truvari_vcf, None)
-                vd_rec_next = next(vcfdist_vcf, None)
-                while vd_rec_next != None and vd_rec_next.genotype(name)['BD'] == None: # skip other callset
-                    vd_rec_next = next(vcfdist_vcf, None)
-                while tv_rec_next != None and tv_rec_next.ALT[0] == "*": # skip nested var
-                    tv_rec_next = next(truvari_vcf, None)
-
-                # test if swapping causes matches
-                if tv_rec.REF == vd_rec_next.REF and \
-                        tv_rec.ALT[0] == vd_rec_next.ALT[0] and \
-                        tv_rec_next.REF == vd_rec.REF and \
-                        tv_rec_next.ALT[0] == vd_rec.ALT[0]:
-                    # 1: tv_rec, vd_rec_next
-                    size1 = get_size(tv_rec.REF, tv_rec.ALT[0])
-                    vd_type1 = get_vd_type(float(vd_rec_next.genotype(name)['BC']))
-                    tv_type1 = get_tv_type(tv_rec_next.genotype(name)['BD'], tv_rec.INFO['PctSeqSimilarity'])
-                    counts[size1][vd_type1][tv_type1] += 1
-                    # 2: tv_rec_next, vd_rec
-                    size2 = get_size(tv_rec_next.REF, tv_rec_next.ALT[0])
-                    vd_type2 = get_vd_type(float(vd_rec.genotype(name)['BC']))
-                    tv_type2 = get_tv_type(tv_rec_next.genotype(name)['BD'], tv_rec.INFO['PctSeqSimilarity'])
-                    counts[size2][vd_type2][tv_type2] += 1
-                    tv_used, vd_used = True, True
-                else:
-                    print("ERROR: failed to match")
-
-                    # discard current two, pretend we haven't looked at next two
-                    counts[size][VD_NONE][TV_NONE] += 2
-                    tv_rec = tv_rec_next
-                    vd_rec = vd_rec_next
-
-
-        elif vd_pos < tv_pos: # vcfdist only
-            vd_used = True
-            size = get_size(vd_rec.REF, vd_rec.ALT[0])
-            if do_print: 
-                print(f"   VD {name} {vd_rec.genotype(name)['GT']} {vd_rec.CHROM}:{vd_rec.POS}\t{vd_rec.REF}\t{vd_rec.ALT[0]}\t")
-            if size != SZ_SNP:
-                print(f"   VD {name} {vd_rec.genotype(name)['GT']} {vd_rec.CHROM}:{vd_rec.POS}\t{vd_rec.REF}\t{vd_rec.ALT[0]}\t")
-                print("WARN: vcfdist only, not SNP")
-            vd_type = get_vd_type(float(vd_rec.genotype(name)['BC']))
-            tv_type = TV_NONE
-            counts[size][vd_type][tv_type] += 1
-
-        elif tv_pos < vd_pos: # truvari only
-            print(f"TV    {name} {tv_rec.genotype(name)['GT']} {tv_rec.CHROM}:{tv_rec.POS}\t{tv_rec.REF}\t{tv_rec.ALT[0]}")
-            print("WARN: Truvari only")
-            tv_used = True
-
-            # skip unphased truvari variants
-            gt = tv_rec.genotype(name)['GT']
-            if gt[1] == '/' and gt[0] != gt[2]:
-                continue
-
-            size = get_size(tv_rec.REF, tv_rec.ALT[0])
-            vd_type = VD_NONE
-            tv_type = get_tv_type(tv_rec.genotype(name)['BD'], tv_rec.INFO['PctSeqSimilarity'])
-            counts[size][vd_type][tv_type] += 1
-
-            # skip if info unavailable
-            if tv_rec.INFO['PctSeqSimilarity'] == None or \
-                    tv_rec.INFO['PctSizeSimilarity'] == None or \
-                    tv_rec.INFO['PctRecOverlap'] == None:
-                counts[size][vd_type][TV_FP] += 1
-                continue
- 
-    for size_idx in range(SZ_DIMS):
-        fig, ax = plt.subplots()
-        ax.matshow(np.log(counts[size_idx,1:,1:] + 0.1), cmap="Blues")
-        plt.title(f"{name} {sizes[size_idx]} Confusion Matrix")
-        plt.ylabel("vcfdist")
-        ax.set_yticks(list(range(VD_DIMS-1)))
-        ax.set_yticklabels(vd_cats[1:])
-        plt.xlabel("Truvari")
-        ax.set_xticks(list(range(TV_DIMS-1)))
-        ax.set_xticklabels(tv_cats[1:])
-        for (i,j), z in np.ndenumerate(counts[size_idx,1:,1:]):
-            ax.text(j, i, f"{int(z)}", ha='center', va='center',
-                bbox=dict(boxstyle='round', facecolor='white', edgecolor='0.3'))
-        plt.savefig(f"img/tv_vd_{callset}_{size_idx}_cm.png", dpi=200)