diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
index 62264fdd..d9692fde 100644
--- a/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
@@ -1,18 +1,18 @@
 {
-    "TP": 197,
+    "TP": 194,
     "TN": 15,
-    "FP": 11,
-    "FN": 2,
+    "FP": 13,
+    "FN": 3,
     "base P": 201,
     "base N": 24,
     "comp P": 210,
     "comp N": 15,
-    "PPV": 0.9380952380952381,
-    "TPR": 0.9800995024875622,
+    "PPV": 0.9238095238095239,
+    "TPR": 0.9651741293532339,
     "TNR": 0.625,
     "NPV": 1.0,
-    "ACC": 0.9422222222222222,
-    "BA": 0.8025497512437811,
-    "F1": 0.9586374695863747,
+    "ACC": 0.9288888888888889,
+    "BA": 0.7950870646766169,
+    "F1": 0.9440389294403894,
     "UND": 0
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt
index 894fb581..16737be9 100644
--- a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt
+++ b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt
@@ -113,7 +113,7 @@ chr20	53913028	53913352	2	2	0	0	False	2	2	0	0	TP
 chr20	54690771	54690873	2	2	0	0	False	2	2	0	0	TP
 chr20	55532159	55533378	1	1	0	0	False	1	1	0	0	TP
 chr20	55624482	55625807	6	6	6	0	True	11	11	0	0	TP
-chr20	55627344	55628450	7	7	4	0	True	8	8	0	0	TP
+chr20	55627344	55628450	7	7	4	0	True	7	7	0	1	FP
 chr20	55943919	55945807	2	2	2	1	True	5	5	0	0	TP
 chr20	56280422	56282114	3	3	6	2	True	10	10	0	0	TP
 chr20	56284258	56284407	2	2	0	0	False	2	2	0	0	TP
@@ -172,7 +172,7 @@ chr20	62875172	62875556	2	2	3	0	True	3	3	0	0	TP
 chr20	62975788	62976224	1	1	0	0	False	1	1	0	0	TP
 chr20	62986310	62986805	2	2	0	0	False	2	2	0	0	TP
 chr20	63027997	63028166	2	2	1	0	True	4	4	0	0	TP
-chr20	63028876	63029402	2	2	0	1	True	2	2	0	0	TP
+chr20	63028876	63029402	2	2	0	1	True	1	1	0	1	FP
 chr20	63049033	63049412	3	3	1	0	True	2	2	0	0	TP
 chr20	63068409	63068799	2	2	0	0	False	2	2	0	0	TP
 chr20	63103249	63103492	1	1	0	0	False	1	1	0	0	TP
@@ -219,7 +219,7 @@ chr20	64090704	64091389	0	0	0	2	False	0	0	0	2	FP
 chr20	64096658	64097164	0	0	0	2	False	0	0	0	2	FP
 chr20	64125109	64127974	3	3	3	0	True	12	12	0	0	TP
 chr20	64131804	64133955	5	5	8	1	True	24	24	0	0	TP
-chr20	64134883	64136386	3	3	1	0	True	4	4	0	0	TP
+chr20	64134883	64136386	3	3	1	0	True	4	4	1	0	FN
 chr20	64157894	64158976	2	2	0	0	False	2	2	0	0	TP
 chr20	64173409	64176529	4	4	7	3	True	18	18	0	0	TP
 chr20	64201854	64202098	3	3	0	0	False	3	3	0	0	TP
diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json
index 11ffccd9..e61085c2 100644
--- a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json
@@ -1,11 +1,11 @@
 {
-    "TP-base": 593,
-    "TP-comp": 593,
-    "FP": 16,
-    "FN": 2,
-    "precision": 0.9737274220032841,
-    "recall": 0.9966386554621849,
-    "f1": 0.9850498338870433,
-    "base cnt": 595,
+    "TP-base": 591,
+    "TP-comp": 591,
+    "FP": 18,
+    "FN": 3,
+    "precision": 0.9704433497536946,
+    "recall": 0.9949494949494949,
+    "f1": 0.9825436408977556,
+    "base cnt": 594,
     "comp cnt": 609
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json
index 6003cac7..1be00983 100644
--- a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json
@@ -1,18 +1,18 @@
 {
-    "TP": 17,
+    "TP": 15,
     "TN": 6,
-    "FP": 23,
+    "FP": 25,
     "FN": 58,
     "base P": 76,
     "base N": 16,
     "comp P": 85,
     "comp N": 7,
-    "PPV": 0.2,
-    "TPR": 0.2236842105263158,
+    "PPV": 0.17647058823529413,
+    "TPR": 0.19736842105263158,
     "TNR": 0.375,
     "NPV": 0.8571428571428571,
-    "ACC": 0.25,
-    "BA": 0.2993421052631579,
-    "F1": 0.2111801242236025,
+    "ACC": 0.22826086956521738,
+    "BA": 0.2861842105263158,
+    "F1": 0.1863354037267081,
     "UND": 0
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt
index ee39c2f5..9ff23aa1 100644
--- a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt
+++ b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt
@@ -15,8 +15,8 @@ chr20	16395201	16395373	3	3	1	0	False	3	3	1	0	FN
 chr20	17081293	17081365	2	2	1	0	False	2	2	1	0	FN
 chr20	18209139	18210134	3	3	2	1	True	3	3	0	1	FP
 chr20	20296014	20296330	2	2	2	1	True	5	5	0	0	TP
-chr20	20320339	20320519	1	1	2	1	True	3	3	0	0	TP
-chr20	20337285	20337624	1	1	6	2	True	1	1	0	0	TP
+chr20	20320339	20320519	1	1	2	1	True	1	1	0	1	FP
+chr20	20337285	20337624	1	1	6	2	True	2	2	0	1	FP
 chr20	20354912	20355435	3	3	1	0	False	3	3	1	0	FN
 chr20	20356530	20357810	4	4	8	1	True	8	8	2	0	FN
 chr20	21120298	21120461	2	2	1	0	False	2	2	1	0	FN
@@ -46,7 +46,7 @@ chr20	53204099	53204252	2	2	2	1	True	0	0	0	0	TN
 chr20	55624808	55625652	6	6	6	0	False	6	6	6	0	FN
 chr20	55627638	55628305	7	7	4	0	False	7	7	4	0	FN
 chr20	55944272	55945175	2	2	2	1	True	1	1	2	0	FN
-chr20	56280541	56281913	3	3	6	2	True	4	4	2	1	FN,FP
+chr20	56280541	56281913	3	3	6	2	True	3	3	2	1	FN,FP
 chr20	57090868	57091166	1	1	2	0	False	1	1	2	0	FN
 chr20	57110450	57110593	2	2	1	0	False	2	2	1	0	FN
 chr20	57190256	57190428	0	0	3	1	True	0	0	0	0	TN
@@ -67,7 +67,7 @@ chr20	62057602	62058768	1	1	3	1	True	1	1	0	0	TP
 chr20	62270413	62270827	1	1	3	1	True	3	3	0	0	TP
 chr20	62321396	62321730	2	2	3	0	False	2	2	3	0	FN
 chr20	62349641	62349826	1	1	5	1	True	0	0	2	1	FN,FP
-chr20	62360410	62360602	0	0	8	2	True	2	2	2	1	FN,FP
+chr20	62360410	62360602	0	0	8	2	True	0	0	6	1	FN,FP
 chr20	62830650	62830697	2	2	1	1	True	1	1	0	0	TP
 chr20	62875241	62875404	2	2	3	0	False	2	2	3	0	FN
 chr20	63028066	63029030	4	4	1	1	True	2	2	0	0	TP
diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json
index c4e13143..1a23dd9a 100644
--- a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json
@@ -1,11 +1,11 @@
 {
-    "TP-base": 408,
-    "TP-comp": 408,
-    "FP": 35,
-    "FN": 108,
-    "precision": 0.9209932279909706,
-    "recall": 0.7906976744186046,
-    "f1": 0.8508863399374348,
+    "TP-base": 404,
+    "TP-comp": 404,
+    "FP": 37,
+    "FN": 112,
+    "precision": 0.9160997732426304,
+    "recall": 0.7829457364341085,
+    "f1": 0.8443051201671891,
     "base cnt": 516,
-    "comp cnt": 443
+    "comp cnt": 441
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json
index 13f20637..de10db40 100644
--- a/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_two/refine.region_summary.json
@@ -1,18 +1,18 @@
 {
-    "TP": 120,
+    "TP": 118,
     "TN": 3,
-    "FP": 6,
-    "FN": 0,
+    "FP": 7,
+    "FN": 1,
     "base P": 121,
     "base N": 8,
     "comp P": 126,
     "comp N": 3,
-    "PPV": 0.9523809523809523,
-    "TPR": 0.9917355371900827,
+    "PPV": 0.9365079365079365,
+    "TPR": 0.9752066115702479,
     "TNR": 0.375,
     "NPV": 1.0,
-    "ACC": 0.9534883720930233,
-    "BA": 0.6833677685950413,
-    "F1": 0.97165991902834,
+    "ACC": 0.937984496124031,
+    "BA": 0.6751033057851239,
+    "F1": 0.9554655870445344,
     "UND": 0
 }
\ No newline at end of file
diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt
index 6e077594..1d4dd76e 100644
--- a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt
+++ b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt
@@ -97,7 +97,7 @@ chr20	62830612	62830838	2	2	1	1	True	2	2	0	0	TP
 chr20	62875172	62875556	2	2	3	0	True	3	3	0	0	TP
 chr20	62986310	62986805	2	2	0	0	False	2	2	0	0	TP
 chr20	63027997	63028166	2	2	1	0	True	4	4	0	0	TP
-chr20	63028876	63029402	2	2	0	1	True	2	2	0	0	TP
+chr20	63028876	63029402	2	2	0	1	True	1	1	0	1	FP
 chr20	63049033	63049412	3	3	1	0	True	2	2	0	0	TP
 chr20	63068409	63068799	2	2	0	0	False	2	2	0	0	TP
 chr20	63103249	63103492	1	1	0	0	False	1	1	0	0	TP
@@ -125,6 +125,6 @@ chr20	64090704	64091389	0	0	0	2	False	0	0	0	2	FP
 chr20	64096658	64097164	0	0	0	2	False	0	0	0	2	FP
 chr20	64125109	64127974	3	3	3	0	True	12	12	0	0	TP
 chr20	64131804	64133955	5	5	8	1	True	24	24	0	0	TP
-chr20	64134883	64136386	3	3	1	0	True	4	4	0	0	TP
+chr20	64134883	64136386	3	3	1	0	True	4	4	1	0	FN
 chr20	64173409	64176529	4	4	7	3	True	18	18	0	0	TP
 chr20	64233048	64233545	2	2	0	0	False	2	2	0	0	TP
diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json
index 16f15c2b..6a256452 100644
--- a/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json
+++ b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json
@@ -1,11 +1,11 @@
 {
-    "TP-base": 406,
-    "TP-comp": 406,
-    "FP": 11,
-    "FN": 0,
-    "precision": 0.973621103117506,
-    "recall": 1.0,
-    "f1": 0.9866342648845686,
+    "TP-base": 405,
+    "TP-comp": 405,
+    "FP": 12,
+    "FN": 1,
+    "precision": 0.9712230215827338,
+    "recall": 0.9975369458128078,
+    "f1": 0.9842041312272175,
     "base cnt": 406,
     "comp cnt": 417
 }
\ No newline at end of file