New TruScore and INS RecOvl

TruScore is calculated differently and INS now have a reciprocal overlap computed.
ACEnglish · Dec 21, 2021 · f0a6088 · f0a6088
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commit f0a6088
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Showing 24 changed files with 116 additions and 120 deletions.
diff --git a/repo_utils/test_files/answer_key/bench12/fn.vcf b/repo_utils/test_files/answer_key/bench12/fn.vcf
@@ -47,11 +47,11 @@
 ##INFO=<ID=MatchId,Number=1,Type=String,Description="Id to help tie base/comp calls together {chunkid}.{baseid}.{compid}">
 ##INFO=<ID=Multi,Number=0,Type=Flag,Description="Call is false due to non-multimatching">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA24385
-chr20	278930	.	C	CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG	60	.	QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.662277;PctSizeSimilarity=0.338858;PctRecOverlap=0;SizeDiff=-359;StartDistance=-139;EndDistance=-139;TruScore=41;MatchId=3.0.0;Multi	GT:PL:DP	0/1:7,9,6:23,9
-chr20	279062	.	G	GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT	60	.	QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139;PctSeqSimilarity=0.419771;PctSizeSimilarity=0.255985;PctRecOverlap=0;SizeDiff=-404;StartDistance=-7;EndDistance=-7;TruScore=27;MatchId=3.1.0;Multi	GT:PL:DP	1/0:5,1,4:27,38
+chr20	278930	.	C	CGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGCGGGACGGAGGGAGGGAG	60	.	QNAME=HG002-S9-H2-000001F;QSTART=232485;QSTRAND=+;SVTYPE=INS;SVLEN=184;PctSeqSimilarity=0.662277;PctSizeSimilarity=0.338858;PctRecOverlap=0.3407;SizeDiff=-359;StartDistance=-139;EndDistance=-139;TruScore=44;MatchId=3.0.0;Multi	GT:PL:DP	0/1:7,9,6:23,9
+chr20	279062	.	G	GGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGTGGGAGGGAGGGAGGGAT	60	.	QNAME=HG002-S9-H1-000001F;QSTART=258112;QSTRAND=+;SVTYPE=INS;SVLEN=139;PctSeqSimilarity=0.419771;PctSizeSimilarity=0.255985;PctRecOverlap=0.255985;SizeDiff=-404;StartDistance=-7;EndDistance=-7;TruScore=31;MatchId=3.1.0;Multi	GT:PL:DP	1/0:5,1,4:27,38
 chr20	420665	.	G	GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC	61	.	QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=0.995604;PctSizeSimilarity=0.995595;PctRecOverlap=1;SizeDiff=1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=6.0.0;Multi	GT:PL	0/1:.
-chr20	642300	.	G	GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC	60	.	QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;PctSeqSimilarity=0.81157;PctSizeSimilarity=0.64557;PctRecOverlap=0;SizeDiff=-224;StartDistance=70;EndDistance=70;GTMatch;TruScore=56;MatchId=8.2.1	GT:PL:DP	1/0:5,10,5:44,36
-chr20	641913	.	G	GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA	60	.	QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.611797;PctSizeSimilarity=0.10443;PctRecOverlap=0;SizeDiff=-566;StartDistance=-317;EndDistance=-317;GTMatch;TruScore=33;MatchId=8.0.1;Multi	GT:PL:DP	1/0:7,5,7:34,13
-chr20	642330	.	G	GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC	60	.	QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.431452;PctSizeSimilarity=0.104762;PctRecOverlap=0;SizeDiff=-564;StartDistance=123;EndDistance=123;GTMatch;TruScore=24;MatchId=8.3.0;Multi	GT:PL:DP	0/1:6,1,9:20,25
-chr20	709830	.	G	GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA	60	.	QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;PctSeqSimilarity=0.0637584;PctSizeSimilarity=0.2;PctRecOverlap=0.0106383;SizeDiff=372;StartDistance=71;EndDistance=-22;GTMatch;TruScore=8;MatchId=9.1.0;Multi	GT:PL:DP	1/0:4,8,7:50,48
+chr20	642300	.	G	GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC	60	.	QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;PctSeqSimilarity=0.81157;PctSizeSimilarity=0.64557;PctRecOverlap=0.64613;SizeDiff=-224;StartDistance=70;EndDistance=70;GTMatch;TruScore=70;MatchId=8.2.1	GT:PL:DP	1/0:5,10,5:44,36
+chr20	641913	.	G	GGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGA	60	.	QNAME=HG002-S9-H1-000001F;QSTART=621365;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.597718;PctSizeSimilarity=0.104762;PctRecOverlap=0.0871632;SizeDiff=-564;StartDistance=-294;EndDistance=-294;TruScore=26;MatchId=8.0.0;Multi	GT:PL:DP	1/0:7,5,7:34,13
+chr20	642330	.	G	GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC	60	.	QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.431452;PctSizeSimilarity=0.104762;PctRecOverlap=0.106181;SizeDiff=-564;StartDistance=123;EndDistance=123;GTMatch;TruScore=21;MatchId=8.3.0;Multi	GT:PL:DP	0/1:6,1,9:20,25
+chr20	709830	.	G	GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA	60	.	QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;PctSeqSimilarity=0.0637584;PctSizeSimilarity=0.2;PctRecOverlap=0.202151;SizeDiff=372;StartDistance=71;EndDistance=-22;GTMatch;TruScore=15;MatchId=9.1.0;Multi	GT:PL:DP	1/0:4,8,7:50,48
 chr20	949516	.	CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA	C	60	.	QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=12.0._	GT:PL:DP	0/1:6,6,1:34,8
diff --git a/repo_utils/test_files/answer_key/bench12/fp.vcf b/repo_utils/test_files/answer_key/bench12/fp.vcf
@@ -48,5 +48,5 @@
 ##INFO=<ID=Multi,Number=0,Type=Flag,Description="Call is false due to non-multimatching">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 chr20	380878	.	T	TGATTAGCTCCGGTTTGCATCACCCGGACCGGGGGATTAGCTCCGGTTTGCATCACCCGGACCGGGG	60	.	QNAME=cluster19_000000F;QSTART=25381150;QSTRAND=-;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=.;PctSizeSimilarity=.;PctRecOverlap=.;SizeDiff=.;StartDistance=.;EndDistance=.;TruScore=.;MatchId=5._.0	GT:PL:AD	1/0:8,3,9:38,14
-chr20	642230	.	T	TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG	60	.	QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.81157;PctSizeSimilarity=0.64557;PctRecOverlap=0;SizeDiff=-224;StartDistance=70;EndDistance=70;GTMatch;TruScore=56;MatchId=8.2.1	GT:PL:AD	1/0:7,5,6:16,7
-chr20	764537	.	A	AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT	60	.	QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.80203;PctSizeSimilarity=0.666667;PctRecOverlap=1;SizeDiff=39;StartDistance=0;EndDistance=0;TruScore=81;MatchId=11.0.0;Multi	GT:PL:AD	1/0:5,4,9:13,8
+chr20	642230	.	T	TGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTG	60	.	QNAME=cluster19_000000F;QSTART=25119065;QSTRAND=-;SVTYPE=INS;SVLEN=632;PctSeqSimilarity=0.81157;PctSizeSimilarity=0.64557;PctRecOverlap=0.64613;SizeDiff=-224;StartDistance=70;EndDistance=70;GTMatch;TruScore=70;MatchId=8.2.1	GT:PL:AD	1/0:7,5,6:16,7
+chr20	764537	.	A	AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT	60	.	QNAME=cluster19_000000F;QSTART=24996803;QSTRAND=-;SVTYPE=INS;SVLEN=78;PctSeqSimilarity=0.80203;PctSizeSimilarity=0.666667;PctRecOverlap=0.675214;SizeDiff=39;StartDistance=0;EndDistance=0;TruScore=71;MatchId=11.0.0;Multi	GT:PL:AD	1/0:5,4,9:13,8
diff --git a/repo_utils/test_files/answer_key/bench12/log.txt b/repo_utils/test_files/answer_key/bench12/log.txt
@@ -1,5 +1,5 @@
-2021-10-17 23:27:02,980 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/input1.vcf.gz -c repo_utils/test_files/input2.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench12/
-2021-10-17 23:27:02,981 [INFO] Params:
+2021-12-21 13:57:48,338 [INFO] Running /data/truvari/__main__.py bench -b repo_utils/test_files/input1.vcf.gz -c repo_utils/test_files/input2.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench12/
+2021-12-21 13:57:48,340 [INFO] Params:
 {
     "base": "repo_utils/test_files/input1.vcf.gz",
     "comp": "repo_utils/test_files/input2.vcf.gz",
@@ -27,11 +27,11 @@
     "includebed": null,
     "multimatch": false
 }
-2021-10-17 23:27:02,982 [INFO] Truvari version: 3.1.0-dev
-2021-10-17 23:27:03,310 [INFO] Zipped 3934 variants. Counter({'base': 2151, 'comp': 1783})
-2021-10-17 23:27:03,312 [INFO] 13 chunks of 30 variants. Counter({'base': 16, 'comp': 14})
-2021-10-17 23:27:03,316 [INFO] Results peek: 8 TP-base 8 FN 50.00% Recall
-2021-10-17 23:27:03,318 [INFO] Stats: {
+2021-12-21 13:57:48,340 [INFO] Truvari version: 3.1.0-dev
+2021-12-21 13:57:48,448 [INFO] Zipped 3934 variants. Counter({'base': 2151, 'comp': 1783})
+2021-12-21 13:57:48,450 [INFO] 13 chunks of 3934 variants. Counter({'__filtered': 3904, 'base': 16, 'comp': 14})
+2021-12-21 13:57:48,455 [INFO] Results peek: 8 TP-base 8 FN 50.00% Recall
+2021-12-21 13:57:48,456 [INFO] Stats: {
     "TP-base": 8,
     "TP-call": 8,
     "FP": 3,
@@ -47,4 +47,4 @@
     "TP-base_FP-gt": 5,
     "gt_concordance": 0.375
 }
-2021-10-17 23:27:03,323 [INFO] Finished bench
+2021-12-21 13:57:48,460 [INFO] Finished bench
diff --git a/repo_utils/test_files/answer_key/bench12/tp-base.vcf b/repo_utils/test_files/answer_key/bench12/tp-base.vcf
@@ -47,11 +47,11 @@
 ##INFO=<ID=MatchId,Number=1,Type=String,Description="Id to help tie base/comp calls together {chunkid}.{baseid}.{compid}">
 ##INFO=<ID=Multi,Number=0,Type=Flag,Description="Call is false due to non-multimatching">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA24385
-chr20	149013	.	A	ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC	60	.	QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.997024;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;GTMatch;TruScore=74;MatchId=1.0.0	GT:PL:DP	1/1:8,8,5:15,29
-chr20	279069	.	A	AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC	60	.	QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438;PctSeqSimilarity=0.873856;PctSizeSimilarity=0.80663;PctRecOverlap=1;SizeDiff=-105;StartDistance=0;EndDistance=0;TruScore=88;MatchId=3.2.0	GT:PL:DP	0/1:7,10,7:12,48
+chr20	149013	.	A	ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC	60	.	QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.997024;PctSizeSimilarity=1;PctRecOverlap=0;SizeDiff=0;StartDistance=-82;EndDistance=-82;GTMatch;TruScore=66;MatchId=1.0.0	GT:PL:DP	1/1:8,8,5:15,29
+chr20	279069	.	A	AGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGACGGAGGGACGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGCGGGAGGGCGGGACGGAGGGACGGAGGGAGGGCGGGACGGAGGGCGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGACGGAGGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGAGGGACGGAGGGCGGGACGGAGGGAGGGAGGGCGGAGGGAGGGAGGGCGGGACGGAGGGAGGGAGGGCGGGAGGGATGGAGGGAGGGAGGGCGGGACGGAGGGAGGGC	60	.	QNAME=HG002-S9-H2-000001F;QSTART=232808;QSTRAND=+;SVTYPE=INS;SVLEN=438;PctSeqSimilarity=0.873856;PctSizeSimilarity=0.80663;PctRecOverlap=0.808471;SizeDiff=-105;StartDistance=0;EndDistance=0;TruScore=82;MatchId=3.2.0	GT:PL:DP	0/1:7,10,7:12,48
 chr20	306268	.	A	ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC	60	.	QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=0.997159;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=99;MatchId=4.0.0	GT:PL:DP	1/1:2,7,2:17,31
 chr20	420665	.	G	GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC	60	.	QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=6.1.0	GT:PL:DP	1/0:4,8,6:32,9
 chr20	613783	.	TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG	T	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=7.0.0	GT:PL:DP	1/1:6,8,8:40,41
-chr20	642207	.	T	TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG	60	.	QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;PctSeqSimilarity=0.88173;PctSizeSimilarity=0.795238;PctRecOverlap=1;SizeDiff=-129;StartDistance=0;EndDistance=0;GTMatch;TruScore=88;MatchId=8.1.0	GT:PL:DP	0/1:5,9,1:7,43
+chr20	642207	.	T	TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG	60	.	QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;PctSeqSimilarity=0.88173;PctSizeSimilarity=0.795238;PctRecOverlap=0.793978;SizeDiff=-129;StartDistance=0;EndDistance=0;GTMatch;TruScore=82;MatchId=8.1.0	GT:PL:DP	0/1:5,9,1:7,43
 chr20	709759	.	AGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCC	A	60	.	QNAME=HG002-S9-H2-000001F;QSTART=664783;QSTRAND=+;SVTYPE=DEL;SVLEN=-93;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=9.0.0	GT:PL:DP	0/1:9,6,6:13,31
 chr20	764537	.	A	AGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAAGGGGAGAATCCCCCACCTAAGGGGAGAGCCCCCACCTAT	60	.	QNAME=HG002-S9-H1-000001F;QSTART=744872;QSTRAND=+;SVTYPE=INS;SVLEN=117;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=11.0.1	GT:PL:DP	1/1:2,1,5:40,30