# HG changeset patch
# User artbio
# Date 1613347182 0
# Node ID ad8853ee9909af9f7f4d3f446320d3d36636a946
# Parent  bd4135caa3fa1592e0194c15eb1c2c7e1f2aff99
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"

diff -r bd4135caa3fa -r ad8853ee9909 lumpy_smoove.xml
--- a/lumpy_smoove.xml	Fri Sep 25 10:43:20 2020 +0000
+++ b/lumpy_smoove.xml	Sun Feb 14 23:59:42 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy5">
+<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy6">
     <description>find structural variants using the smoove workflow</description>
     <macros>
         <import>macro_lumpy_smoove.xml</import>
@@ -102,7 +102,7 @@
             <param name="choices" value="yes"/>
             <param name="bedmask" value="exclude.bed"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="8"/>
+            <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="12"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -112,7 +112,7 @@
             <param name="choices" value="yes"/>
             <param name="bedmask" value="exclude.bed"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="8"/>
+            <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="12"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -121,7 +121,7 @@
             <param name="tumor_bam" value="celegans_RG_2.bam"/>
             <param name="choices" value="no"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="8"/>
+            <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="12"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -130,7 +130,7 @@
             <param name="tumor_bam" value="celegans_RG_1.bam"/>
             <param name="choices" value="no"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="8"/>
+            <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="12"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -139,7 +139,7 @@
             <param name="tumor_bam" value="celegans_RG_2.bam"/>
             <param name="choices" value="no"/>
             <param name="prpos" value="yes"/>
-            <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="8"/>
+            <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="12"/>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
@@ -148,7 +148,7 @@
             <param name="single_bam" value="celegans_RG_1.bam"/>
             <param name="choices" value="no"/>
             <param name="prpos" value="no"/>
-            <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="8"/>
+            <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="12"/>
         </test>
     </tests>
 
diff -r bd4135caa3fa -r ad8853ee9909 test-data/test_vcf2hrdetect.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_vcf2hrdetect.tab	Sun Feb 14 23:59:42 2021 +0000
@@ -0,0 +1,180 @@
+chr1	pos1	chr2	pos2	type
+1	28515659	19	24027918	TRA
+1	42552553	4	44842163	TRA
+1	44059282	1	44059890	INV
+1	64897140	6	159204434	TRA
+1	66804423	13	59377693	TRA
+1	80794627	1	80795137	INV
+1	91151631	8	85437297	TRA
+1	105428633	7	93357413	TRA
+1	119401195	15	51189306	TRA
+1	168024578	19	24033135	TRA
+1	221827800	13	61315891	TRA
+1	234805693	16	59323740	TRA
+2	12019022	7	52399206	TRA
+2	77358259	18	59713754	TRA
+2	78091959	4	174044216	TRA
+2	153997618	17	74377266	TRA
+2	160095376	2	160095824	INV
+2	178351450	19	52567370	TRA
+2	178351470	19	52567638	TRA
+2	204273805	4	68944782	TRA
+3	12818457	5	144122990	TRA
+3	38399708	8	75876952	TRA
+3	48372309	7	32225987	TRA
+3	54428366	12	28226427	TRA
+3	75960769	11	130675918	TRA
+3	105828859	5	141379626	TRA
+3	151748833	3	176444683	INV
+3	158034493	6	32688592	TRA
+3	182298978	11	94948981	TRA
+3	182299013	9	1940734	TRA
+3	184156702	20	231409	TRA
+3	192376521	10	65545580	TRA
+4	81136688	6	68923562	TRA
+4	99513602	6	32589570	TRA
+4	162642267	X	3599701	TRA
+4	162642407	X	3599706	TRA
+4	175534267	10	123120353	TRA
+4	183256660	8	131547788	TRA
+4	186382139	9	129005120	TRA
+5	5595231	15	52589534	TRA
+5	37709852	7	8663298	TRA
+5	53122606	5	53125511	INV
+5	53122773	5	53125484	INV
+5	54865791	10	75489275	TRA
+5	54865801	10	75489000	TRA
+5	147553039	5	147554616	INV
+5	157223490	5	176652060	INV
+5	157223548	11	3760878	TRA
+5	169597700	5	169598748	INV
+5	176651964	11	3760899	TRA
+6	17608998	X	117432517	TRA
+6	26625483	7	68758443	TRA
+6	37295025	12	22085955	TRA
+6	74156485	14	71480241	TRA
+6	107307808	8	105231718	TRA
+6	161336425	7	85956546	TRA
+7	70420972	7	70438890	INV
+7	98015910	X	136092975	TRA
+7	111053752	12	108203254	TRA
+7	127930431	16	76865795	TRA
+7	156387047	7	156387226	INV
+8	30145409	17	7167951	TRA
+8	59616000	16	3354097	TRA
+8	96265720	19	18835613	TRA
+8	140475500	12	58359059	TRA
+8	140475502	11	56303340	TRA
+9	127885505	18	71711520	TRA
+9	141058509	10	107209	TRA
+10	51019958	12	46175132	TRA
+10	59256942	10	59257951	INV
+10	59257660	10	59257985	INV
+10	68673027	16	59976476	TRA
+10	132635667	10	132636051	INV
+11	106143090	11	106143794	INV
+12	104359630	12	125801144	INV
+13	35787786	X	11952984	TRA
+14	47118175	14	63226299	INV
+14	65842539	14	65843134	INV
+14	90299534	14	90302487	INV
+14	106484224	15	22486809	TRA
+15	75867566	16	89281701	TRA
+21	32956225	X	47183861	TRA
+X	114216686	X	114544524	INV
+1	14436660	1	14438563	DUP
+1	43694066	1	43695538	DEL
+1	80221789	1	80223032	DEL
+1	92232065	1	92233362	DEL
+2	18118870	2	18120031	DEL
+2	19002880	2	19003387	DEL
+2	34797601	2	34801579	DEL
+2	34965732	2	34967261	DEL
+2	48990532	2	48991191	DEL
+2	76773562	2	76775444	DEL
+2	120417073	2	120418454	DUP
+2	125766561	2	125768399	DUP
+2	156774338	2	156776256	DEL
+2	179315148	2	179315689	DEL
+2	189119618	2	189120979	DEL
+3	32203783	3	32204153	DEL
+3	124936235	3	124937163	DEL
+3	129763389	3	129806742	DEL
+3	144517821	3	144518457	DEL
+3	190785116	3	190789319	DEL
+4	73831211	4	73831818	DEL
+4	88268261	4	88274334	DEL
+4	102787795	4	102788358	DEL
+4	144573271	4	144573612	DEL
+4	151011309	4	151011648	DUP
+5	1178285	5	1180725	DEL
+5	26796704	5	26801897	DEL
+5	95966521	5	95967361	DEL
+5	103062313	5	103062635	DEL
+5	108595090	5	108601127	DEL
+5	127336004	5	127336923	DEL
+5	178109055	5	178113407	DEL
+6	20169115	6	108322150	DUP
+6	32315438	6	32316258	DEL
+6	37294925	6	37295284	DEL
+6	65022877	6	65023371	DUP
+6	72863847	6	72873539	DEL
+6	74932726	6	74933069	DEL
+6	89921735	6	89922171	DEL
+6	136589486	6	136590574	DEL
+7	65857652	7	65860106	DEL
+7	76134084	7	76140082	DEL
+7	86615393	7	86615759	DEL
+7	93541820	7	93542546	DEL
+7	97993595	7	97993987	DEL
+7	100056291	7	129157154	DUP
+7	151230203	7	151231867	DEL
+8	11245570	8	11247212	DEL
+8	14588058	8	14588822	DEL
+8	16821879	8	16822259	DEL
+8	118980771	8	118981151	DEL
+9	104182136	9	104182429	DUP
+9	104714849	9	104724476	DEL
+9	110033442	9	110035532	DEL
+9	139427511	9	139427797	DEL
+10	35593223	10	35593548	DEL
+10	45158118	10	45158533	DEL
+10	55893654	10	55894125	DEL
+10	87242583	10	87243046	DUP
+10	132858454	10	132858819	DEL
+10	132988685	10	132991206	DEL
+11	93695221	11	93702091	DEL
+11	97172221	11	97172970	DEL
+11	99185461	11	99186696	DEL
+12	12026417	12	12027146	DEL
+12	30478280	12	30480988	DEL
+13	38071947	13	38085574	DEL
+13	74915300	13	74916746	DEL
+13	89421953	13	89422932	DEL
+14	23105069	14	23107950	DEL
+14	32953296	14	32954345	DEL
+14	41829108	14	41980350	DEL
+14	42486317	14	42486634	DEL
+14	60341404	14	60343237	DEL
+14	61058056	14	61059493	DEL
+14	80106294	14	80115045	DEL
+15	39744398	15	39744849	DEL
+15	62706095	15	62707781	DEL
+16	13294470	16	13296490	DEL
+16	33485944	16	33486280	DEL
+16	69854786	16	69859026	DUP
+16	85302496	16	85304389	DEL
+17	45634774	17	45635284	DEL
+17	46615627	17	46617222	DUP
+17	68159938	17	68160278	DEL
+17	70815221	17	70821355	DEL
+18	39585688	18	39586313	DEL
+18	77309929	18	77312095	DEL
+19	15046341	19	15049471	DEL
+19	51077891	19	51082521	DEL
+20	3821170	20	3825120	DEL
+20	61724700	20	61725614	DEL
+20	62949719	20	62959202	DEL
+22	17770355	22	17779150	DEL
+22	19099927	22	19100621	DEL
+X	55702382	X	55709885	DEL
diff -r bd4135caa3fa -r ad8853ee9909 test-data/test_vcf2hrdetect.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_vcf2hrdetect.vcf	Sun Feb 14 23:59:42 2021 +0000
@@ -0,0 +1,403 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20201029
+##reference=reference.fa
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
+##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
+##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
+##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
+##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
+##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
+##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##ALT=<ID=CNV,Description="Copy number variable region">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
+##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=1,length=249250621>
+##contig=<ID=2,length=243199373>
+##contig=<ID=3,length=198022430>
+##contig=<ID=4,length=191154276>
+##contig=<ID=5,length=180915260>
+##contig=<ID=6,length=171115067>
+##contig=<ID=7,length=159138663>
+##contig=<ID=8,length=146364022>
+##contig=<ID=9,length=141213431>
+##contig=<ID=10,length=135534747>
+##contig=<ID=11,length=135006516>
+##contig=<ID=12,length=133851895>
+##contig=<ID=13,length=115169878>
+##contig=<ID=14,length=107349540>
+##contig=<ID=15,length=102531392>
+##contig=<ID=16,length=90354753>
+##contig=<ID=17,length=81195210>
+##contig=<ID=18,length=78077248>
+##contig=<ID=19,length=59128983>
+##contig=<ID=20,length=63025520>
+##contig=<ID=21,length=48129895>
+##contig=<ID=22,length=51304566>
+##contig=<ID=X,length=155270560>
+##contig=<ID=Y,length=59373566>
+##contig=<ID=MT,length=16569>
+##contig=<ID=GL000207.1,length=4262>
+##contig=<ID=GL000226.1,length=15008>
+##contig=<ID=GL000229.1,length=19913>
+##contig=<ID=GL000231.1,length=27386>
+##contig=<ID=GL000210.1,length=27682>
+##contig=<ID=GL000239.1,length=33824>
+##contig=<ID=GL000235.1,length=34474>
+##contig=<ID=GL000201.1,length=36148>
+##contig=<ID=GL000247.1,length=36422>
+##contig=<ID=GL000245.1,length=36651>
+##contig=<ID=GL000197.1,length=37175>
+##contig=<ID=GL000203.1,length=37498>
+##contig=<ID=GL000246.1,length=38154>
+##contig=<ID=GL000249.1,length=38502>
+##contig=<ID=GL000196.1,length=38914>
+##contig=<ID=GL000248.1,length=39786>
+##contig=<ID=GL000244.1,length=39929>
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+##contig=<ID=GL000202.1,length=40103>
+##contig=<ID=GL000234.1,length=40531>
+##contig=<ID=GL000232.1,length=40652>
+##contig=<ID=GL000206.1,length=41001>
+##contig=<ID=GL000240.1,length=41933>
+##contig=<ID=GL000236.1,length=41934>
+##contig=<ID=GL000241.1,length=42152>
+##contig=<ID=GL000243.1,length=43341>
+##contig=<ID=GL000242.1,length=43523>
+##contig=<ID=GL000230.1,length=43691>
+##contig=<ID=GL000237.1,length=45867>
+##contig=<ID=GL000233.1,length=45941>
+##contig=<ID=GL000204.1,length=81310>
+##contig=<ID=GL000198.1,length=90085>
+##contig=<ID=GL000208.1,length=92689>
+##contig=<ID=GL000191.1,length=106433>
+##contig=<ID=GL000227.1,length=128374>
+##contig=<ID=GL000228.1,length=129120>
+##contig=<ID=GL000214.1,length=137718>
+##contig=<ID=GL000221.1,length=155397>
+##contig=<ID=GL000209.1,length=159169>
+##contig=<ID=GL000218.1,length=161147>
+##contig=<ID=GL000220.1,length=161802>
+##contig=<ID=GL000213.1,length=164239>
+##contig=<ID=GL000211.1,length=166566>
+##contig=<ID=GL000199.1,length=169874>
+##contig=<ID=GL000217.1,length=172149>
+##contig=<ID=GL000216.1,length=172294>
+##contig=<ID=GL000215.1,length=172545>
+##contig=<ID=GL000205.1,length=174588>
+##contig=<ID=GL000219.1,length=179198>
+##contig=<ID=GL000224.1,length=179693>
+##contig=<ID=GL000223.1,length=180455>
+##contig=<ID=GL000195.1,length=182896>
+##contig=<ID=GL000212.1,length=186858>
+##contig=<ID=GL000222.1,length=186861>
+##contig=<ID=GL000200.1,length=187035>
+##contig=<ID=GL000193.1,length=189789>
+##contig=<ID=GL000194.1,length=191469>
+##contig=<ID=GL000225.1,length=211173>
+##contig=<ID=GL000192.1,length=547496>
+##smoove_version=0.2.5
+##smoove_count_stats=TARGET-21-PAMXZY-15A-01D:0,646270,0,297568
+##smoove_count_stats=TARGET-21-PAMXZY-09A-03D:0,504761,0,141470
+##source=LUMPY
+##bcftools_annotateVersion=1.10.2+htslib-1.10.2
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Thu Oct 29 18:30:42 2020
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##bcftools_viewVersion=1.10.2+htslib-1.10.2
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Thu Oct 29 18:30:42 2020
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TARGET-21-PAMXZY-15A-01D	TARGET-21-PAMXZY-09A-03D
+1	14436660	4	N	<DUP>	40.38	.	SVTYPE=DUP;SVLEN=1903;END=14438563;STRANDS=-+:11;IMPRECISE;CIPOS=-219,29;CIEND=-30,224;CIPOS95=-93,4;CIEND95=-4,95;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:19:0.05:-0,-2,-4:21:21:0:21:0:21:0:0:0:0:0	0/1:40:40.33:-7,-3,-8:110:98:11:97:10:44:0:0:53:10:0.093
+1	28515659	1971_1	N	N]19:24027918]	194.49	.	SVTYPE=BND;STRANDS=++:12;IMPRECISE;CIPOS=-24,212;CIEND=-30,228;CIPOS95=-4,93;CIEND95=-4,73;MATEID=1971_2;EVENT=1971;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:162:0:-0,-16,-54:56:55:0:54:0:23:0:0:31:0:0	0/1:194:194.49:-27,-8,-47:76:61:14:61:14:0:0:0:61:14:0.19
+1	42552553	1942_1	N	N[4:44842163[	59.54	.	SVTYPE=BND;STRANDS=+-:7;IMPRECISE;CIPOS=-15,285;CIEND=-238,29;CIPOS95=-1,137;CIEND95=-86,5;MATEID=1942_2;EVENT=1942;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:57:0:-3,-9,-34:40:37:2:37:2:0:0:0:37:2:0.051	0/1:59:59.54:-16,-10,-51:71:61:9:61:9:0:0:0:61:9:0.13
+1	43694066	15	N	<DEL>	353.17	.	SVTYPE=DEL;SVLEN=-1472;END=43695538;STRANDS=+-:26;IMPRECISE;CIPOS=-30,203;CIEND=-202,29;CIPOS95=-7,39;CIEND95=-55,4;SU=26;PE=26;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:60:0:-5,-11,-43:52:48:4:47:3:23:0:1:24:2:0.06	0/1:200:353.17:-47,-11,-74:124:99:24:98:24:47:0:2:51:22:0.2
+1	44059282	17_1	N	N]1:44059890]	50.66	.	SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-30,193;CIEND=-30,225;CIPOS95=-7,65;CIEND95=-4,94;MATEID=17_2;EVENT=17;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:36:0:-3,-7,-27:33:30:2:30:2:0:0:0:30:2:0.062	0/1:50:50.65:-13,-8,-38:54:46:7:46:7:0:0:0:46:7:0.13
+1	44059890	17_2	N	N]1:44059282]	50.66	.	SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-30,225;CIEND=-30,193;CIPOS95=-4,94;CIEND95=-7,65;MATEID=17_1;EVENT=17;SECONDARY;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:36:0:-3,-7,-27:33:30:2:30:2:0:0:0:30:2:0.062	0/1:50:50.65:-13,-8,-38:54:46:7:46:7:0:0:0:46:7:0.13
+1	64897140	1952_1	N	[6:159204434[N	35.75	.	SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-289,21;CIEND=-250,29;CIPOS95=-137,3;CIEND95=-106,5;MATEID=1952_2;EVENT=1952;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:75:0:-0,-8,-25:27:26:0:25:0:9:0:0:16:0:0	0/1:35:35.75:-9,-6,-28:39:33:5:33:5:0:0:0:33:5:0.13
+1	66804423	1961_1	N	[13:59377693[N	23.75	.	SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-294,16;CIEND=-240,29;CIPOS95=-142,1;CIEND95=-83,5;MATEID=1961_2;EVENT=1961;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:12:0.25:-5,-6,-27:35:31:3:31:3:0:0:0:31:3:0.088	0/1:23:23.49:-16,-13,-62:83:73:9:73:9:0:0:0:73:9:0.11
+1	80221789	47	N	<DEL>	116.67	.	SVTYPE=DEL;SVLEN=-1243;END=80223032;STRANDS=+-:12;IMPRECISE;CIPOS=-30,178;CIEND=-194,29;CIPOS95=-5,42;CIEND95=-47,8;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:24:0.02:-5,-8,-31:40:36:4:35:3:13:0:0:22:3:0.079	0/1:116:116.66:-18,-6,-33:52:42:9:42:9:0:0:0:42:9:0.18
+1	80794627	48_1	N	[1:80795137[N	41.32	.	SVTYPE=BND;STRANDS=--:17;IMPRECISE;CIPOS=-193,21;CIEND=-179,21;CIPOS95=-79,2;CIEND95=-65,2;MATEID=48_2;EVENT=48;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:45:0:-5,-9,-38:46:42:3:42:3:0:0:0:42:3:0.067	0/1:41:41.32:-21,-17,-79:107:94:12:94:12:0:0:0:94:12:0.11
+1	80795137	48_2	N	[1:80794627[N	41.32	.	SVTYPE=BND;STRANDS=--:17;IMPRECISE;CIPOS=-179,21;CIEND=-193,21;CIPOS95=-65,2;CIEND95=-79,2;MATEID=48_1;EVENT=48;SECONDARY;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:45:0:-5,-9,-38:46:42:3:42:3:0:0:0:42:3:0.067	0/1:41:41.32:-21,-17,-79:107:94:12:94:12:0:0:0:94:12:0.11
+1	91151631	1956_1	N	N[8:85437297[	53.53	.	SVTYPE=BND;STRANDS=+-:10;IMPRECISE;CIPOS=-25,239;CIEND=-237,25;CIPOS95=-3,111;CIEND95=-101,2;MATEID=1956_2;EVENT=1956;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:171:0:-0,-17,-57:59:58:0:57:0:30:0:0:27:0:0	0/1:53:53.53:-16,-11,-52:73:63:9:63:9:0:0:0:63:9:0.12
+1	92232065	60	N	<DEL>	35.11	.	SVTYPE=DEL;SVLEN=-1297;END=92233362;STRANDS=+-:17;IMPRECISE;CIPOS=-30,298;CIEND=-197,15;CIPOS95=-4,80;CIEND95=-82,4;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:69:0:-5,-12,-46:55:51:3:50:3:24:0:1:26:2:0.057	0/1:35:35.11:-25,-22,-104:140:124:15:123:15:66:0:2:57:13:0.11
+1	105428633	1954_1	N	N[7:93357413[	104.7	.	SVTYPE=BND;STRANDS=+-:9;IMPRECISE;CIPOS=-21,258;CIEND=-225,29;CIPOS95=-2,129;CIEND95=-93,4;MATEID=1954_2;EVENT=1954;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:102:0:-0,-10,-34:36:35:0:34:0:16:0:0:18:0:0	0/1:104:104.7:-16,-5,-29:46:37:8:37:8:0:0:0:37:8:0.18
+1	119401195	1963_1	N	N[15:51189306[	41.32	.	SVTYPE=BND;STRANDS=+-:14;IMPRECISE;CIPOS=-30,271;CIEND=-192,29;CIPOS95=-3,87;CIEND95=-71,6;MATEID=1963_2;EVENT=1963;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:60:0:-5,-11,-43:51:47:3:47:3:0:0:0:47:3:0.06	0/1:41:41.32:-21,-17,-79:107:94:12:94:12:0:0:0:94:12:0.11
+1	168024578	1972_1	N	]19:24033135]N	4.57	.	SVTYPE=BND;STRANDS=-+:8;IMPRECISE;CIPOS=-274,18;CIEND=-30,210;CIPOS95=-129,2;CIEND95=-6,75;MATEID=1972_2;EVENT=1972;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-2,-4,-17:20:18:1:18:1:0:0:0:18:1:0.053	0/1:2:4.56:-9,-8,-38:50:44:5:44:5:0:0:0:44:5:0.1
+1	221827800	1962_1	N	N[13:61315891[	53.72	.	SVTYPE=BND;STRANDS=+-:6;IMPRECISE;CIPOS=-30,271;CIEND=-349,29;CIPOS95=-3,117;CIEND95=-139,3;MATEID=1962_2;EVENT=1962;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:81:0:-0,-8,-27:28:28:0:27:0:14:0:0:13:0:0	0/1:53:53.72:-11,-6,-30:43:36:6:36:6:0:0:0:36:6:0.14
+1	234805693	1969_1	N	N[16:59323740[	20.7	.	SVTYPE=BND;STRANDS=+-:7;IMPRECISE;CIPOS=-30,282;CIEND=-347,29;CIPOS95=-4,98;CIEND95=-138,1;MATEID=1969_2;EVENT=1969;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:138:0:-0,-14,-46:47:47:0:46:0:24:0:0:22:0:0	0/1:20:20.7:-11,-9,-40:54:47:6:47:6:0:0:0:47:6:0.11
+2	12019022	1982_1	N	N]7:52399206]	14.67	.	SVTYPE=BND;STRANDS=++:9;IMPRECISE;CIPOS=-30,221;CIEND=-19,261;CIPOS95=-2,91;CIEND95=-2,131;MATEID=1982_2;EVENT=1982;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:0:-0,-24,-80:81:81:0:80:0:41:0:0:39:0:0	0/1:14:14.67:-14,-12,-57:76:67:8:67:8:0:0:0:67:8:0.11
+2	18118870	172	N	<DEL>	233.63	.	SVTYPE=DEL;SVLEN=-1161;END=18120031;STRANDS=+-:19;IMPRECISE;CIPOS=-22,175;CIEND=-220,29;CIPOS95=-4,69;CIEND95=-53,7;SU=19;PE=19;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:18:0.06:-5,-7,-29:37:33:3:33:3:0:0:0:33:3:0.083	0/1:200:233.57:-29,-5,-35:63:48:14:48:14:0:0:0:48:14:0.23
+2	19002880	174	N	<DEL>	170.16	.	SVTYPE=DEL;SVLEN=-507;END=19003387;STRANDS=+-:20;IMPRECISE;CIPOS=-28,161;CIEND=-255,29;CIPOS95=-6,55;CIEND95=-64,3;SU=20;PE=20;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:0:2.85:-9,-9,-39:53:46:6:45:5:23:0:0:22:5:0.1	0/1:167:167.31:-30,-13,-70:106:89:16:88:16:44:0:3:44:13:0.15
+2	34797601	185	N	<DEL>	212.66	.	SVTYPE=DEL;SVLEN=-3978;END=34801579;STRANDS=+-:14;IMPRECISE;CIPOS=-30,217;CIEND=-207,29;CIPOS95=-4,59;CIEND95=-57,7;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:51:0:-2,-7,-25:28:26:1:26:1:0:0:0:26:1:0.037	0/1:200:212.66:-25,-4,-27:50:37:12:37:12:0:0:0:37:12:0.24
+2	34965732	186	N	<DEL>	182.15	.	SVTYPE=DEL;SVLEN=-1529;END=34967261;STRANDS=+-:20;IMPRECISE;CIPOS=-30,197;CIEND=-288,29;CIPOS95=-4,42;CIEND95=-76,2;SU=20;PE=20;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:66:0:-8,-15,-60:74:68:6:67:5:40:0:2:27:3:0.069	0/1:182:182.15:-35,-16,-88:132:111:20:110:19:55:0:4:55:15:0.15
+2	48990532	193	N	<DEL>	135.43	.	SVTYPE=DEL;SVLEN=-659;END=48991191;STRANDS=+-:17;IMPRECISE;CIPOS=-29,179;CIEND=-264,29;CIPOS95=-3,64;CIEND95=-60,6;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:6:0.93:-5,-6,-25:33:29:3:29:3:0:0:0:29:3:0.094	0/1:134:134.5:-23,-9,-50:76:63:12:63:12:0:0:0:63:12:0.16
+2	76773562	204	N	<DEL>	320.17	.	SVTYPE=DEL;SVLEN=-1882;END=76775444;STRANDS=+-:21;IMPRECISE;CIPOS=-30,145;CIEND=-240,29;CIPOS95=-7,44;CIEND95=-57,3;SU=21;PE=21;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:30:0:-8,-11,-48:63:56:6:55:5:31:0:2:24:3:0.083	0/1:200:320.17:-44,-12,-76:125:101:24:100:23:54:0:6:46:17:0.19
+2	77358259	2004_1	N	N[18:59713754[	4.44	.	SVTYPE=BND;STRANDS=+-:11;IMPRECISE;CIPOS=-19,255;CIEND=-216,28;CIPOS95=-3,122;CIEND95=-83,4;MATEID=2004_2;EVENT=2004;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-3,-6,-24:30:27:2:27:2:0:0:0:27:2:0.069	0/1:2:4.43:-14,-13,-61:80:71:8:71:8:0:0:0:71:8:0.1
+2	78091959	1979_1	N	[4:174044216[N	38.57	.	SVTYPE=BND;STRANDS=--:11;IMPRECISE;CIPOS=-245,12;CIEND=-186,29;CIPOS95=-112,1;CIEND95=-64,6;MATEID=1979_2;EVENT=1979;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:54:0:-2,-7,-26:29:27:1:27:1:0:0:0:27:1:0.036	0/1:38:38.57:-14,-10,-50:68:59:8:59:8:0:0:0:59:8:0.12
+2	120417073	234	N	<DUP>	52.37	.	SVTYPE=DUP;SVLEN=1381;END=120418454;STRANDS=-+:12;IMPRECISE;CIPOS=-331,29;CIEND=-30,171;CIPOS95=-119,3;CIEND95=-4,52;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:74:0:-0,-8,-14:82:81:0:80:0:40:0:0:40:0:0	0/1:44:52.37:-7,-2,-7:95:84:10:84:10:0:0:0:84:10:0.11
+2	125766561	239	N	<DUP>	52.69	.	SVTYPE=DUP;SVLEN=1838;END=125768399;STRANDS=-+:13;IMPRECISE;CIPOS=-186,29;CIEND=-30,312;CIPOS95=-70,6;CIEND95=-3,105;SU=13;PE=13;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:33:0:-2,-5,-12:98:93:5:92:4:46:0:3:46:1:0.042	0/1:52:52.69:-10,-5,-15:186:169:17:168:16:82:0:5:86:11:0.087
+2	153997618	2002_1	N	N[17:74377266[	23.44	.	SVTYPE=BND;STRANDS=+-:14;IMPRECISE;CIPOS=-30,176;CIEND=-220,20;CIPOS95=-6,60;CIEND95=-101,2;MATEID=2002_2;EVENT=2002;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-5,-8,-32:40:36:3:36:3:0:0:0:36:3:0.077	0/1:23:23.43:-17,-15,-70:93:82:10:82:10:0:0:0:82:10:0.11
+2	156774338	269	N	<DEL>	8.81	.	SVTYPE=DEL;SVLEN=-1918;END=156776256;STRANDS=+-:16;IMPRECISE;CIPOS=-30,291;CIEND=-186,29;CIPOS95=-2,86;CIEND95=-73,5;SU=16;PE=16;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:30:0:-8,-11,-48:62:56:6:55:5:30:0:2:25:3:0.083	0/1:8:8.8:-22,-21,-97:129:115:14:114:13:58:0:2:56:11:0.1
+2	160095376	272_1	N	[2:160095824[N	47.58	.	SVTYPE=BND;STRANDS=--:17;IMPRECISE;CIPOS=-256,29;CIEND=-227,29;CIPOS95=-58,5;CIEND95=-84,4;MATEID=272_2;EVENT=272;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:12:0.25:-7,-8,-35:45:40:4:40:4:0:0:0:40:4:0.091	0/1:47:47.33:-21,-16,-77:105:92:12:92:12:0:0:0:92:12:0.12
+2	160095824	272_2	N	[2:160095376[N	47.58	.	SVTYPE=BND;STRANDS=--:17;IMPRECISE;CIPOS=-227,29;CIEND=-256,29;CIPOS95=-84,4;CIEND95=-58,5;MATEID=272_1;EVENT=272;SECONDARY;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:12:0.25:-7,-8,-35:45:40:4:40:4:0:0:0:40:4:0.091	0/1:47:47.33:-21,-16,-77:105:92:12:92:12:0:0:0:92:12:0.12
+2	178351450	2007_1	N	[19:52567370[N	56.6	.	SVTYPE=BND;STRANDS=--:10;IMPRECISE;CIPOS=-283,29;CIEND=-244,28;CIPOS95=-100,4;CIEND95=-104,2;MATEID=2007_2;EVENT=2007;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:45:0:-2,-6,-23:26:24:1:24:1:0:0:0:24:1:0.04	0/1:56:56.6:-15,-9,-44:62:53:8:53:8:0:0:0:53:8:0.13
+2	178351470	2006_1	N	N]19:52567638]	110.71	.	SVTYPE=BND;STRANDS=++:10;IMPRECISE;CIPOS=-30,147;CIEND=-30,187;CIPOS95=-4,36;CIEND95=-6,54;MATEID=2006_2;EVENT=2006;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:84:0:-0,-8,-28:30:29:0:28:0:11:0:0:17:0:0	0/1:110:110.71:-16,-5,-27:44:35:8:35:8:0:0:0:35:8:0.19
+2	179315148	295	N	<DEL>	82.7	.	SVTYPE=DEL;SVLEN=-541;END=179315689;STRANDS=+-:28;IMPRECISE;CIPOS=-22,156;CIEND=-244,29;CIPOS95=-4,69;CIEND95=-48,3;SU=28;PE=28;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:99:0:-6,-16,-63:75:70:5:69:4:36:0:0:33:4:0.055	0/1:82:82.7:-39,-31,-150:205:180:24:179:23:93:0:0:86:23:0.11
+2	189119618	306	N	<DEL>	515.59	.	SVTYPE=DEL;SVLEN=-1361;END=189120979;STRANDS=+-:14;IMPRECISE;CIPOS=-23,182;CIEND=-188,29;CIPOS95=-3,67;CIEND95=-72,3;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:21:0.03:-0,-2,-7:7:7:0:7:0:7:0:0:0:0:0	0/1:185:515.55:-53,-2,-20:59:35:24:35:23:13:0:9:22:14:0.4
+2	204273805	1977_1	N	N]4:68944782]	62.68	.	SVTYPE=BND;STRANDS=++:6;IMPRECISE;CIPOS=-30,269;CIEND=-30,257;CIPOS95=-4,116;CIEND95=-3,96;MATEID=1977_2;EVENT=1977;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:84:0:-0,-8,-28:30:29:0:28:0:15:0:0:13:0:0	0/1:62:62.68:-13,-7,-34:50:42:7:42:7:0:0:0:42:7:0.14
+3	12818457	2017_1	N	N[5:144122990[	90.24	.	SVTYPE=BND;STRANDS=+-:10;IMPRECISE;CIPOS=-30,240;CIEND=-248,26;CIPOS95=-6,73;CIEND95=-117,3;MATEID=2017_2;EVENT=2017;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.51:-2,-3,-11:14:12:1:12:1:0:0:0:12:1:0.077	0/1:89:89.73:-14,-5,-26:41:33:7:33:7:0:0:0:33:7:0.17
+3	32203783	365	N	<DEL>	7.56	.	SVTYPE=DEL;SVLEN=-370;END=32204153;STRANDS=+-:6;IMPRECISE;CIPOS=-30,275;CIEND=-331,29;CIPOS95=-3,125;CIEND95=-132,3;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:6:0.93:-5,-6,-25:33:29:3:29:3:0:0:0:29:3:0.094	0/1:5:6.63:-12,-11,-52:69:61:7:61:7:0:0:0:61:7:0.1
+3	38399708	2022_1	N	[8:75876952[N	69.39	.	SVTYPE=BND;STRANDS=--:7;IMPRECISE;CIPOS=-183,29;CIEND=-278,21;CIPOS95=-61,8;CIEND95=-131,3;MATEID=2022_2;EVENT=2022;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.51:-2,-3,-11:14:12:1:12:1:0:0:0:12:1:0.077	0/1:68:68.88:-9,-2,-10:18:13:4:13:4:0:0:0:13:4:0.24
+3	48372309	2020_1	N	N]7:32225987]	17.6	.	SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-30,202;CIEND=-21,243;CIPOS95=-3,76;CIEND95=-3,120;MATEID=2020_2;EVENT=2020;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:63:0:-2,-8,-29:32:30:1:30:1:0:0:0:30:1:0.032	0/1:17:17.6:-14,-12,-56:75:66:8:66:8:0:0:0:66:8:0.11
+3	54428366	2030_1	N	]12:28226427]N	80.79	.	SVTYPE=BND;STRANDS=-+:9;IMPRECISE;CIPOS=-347,29;CIEND=-30,209;CIPOS95=-126,3;CIEND95=-5,78;MATEID=2030_2;EVENT=2030;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:24:0.02:-2,-4,-16:19:17:1:17:1:0:0:0:17:1:0.056	0/1:80:80.78:-12,-4,-21:34:27:6:27:6:0:0:0:27:6:0.18
+3	75960769	2029_1	N	[11:130675918[N	56.61	.	SVTYPE=BND;STRANDS=--:12;IMPRECISE;CIPOS=-236,22;CIEND=-202,26;CIPOS95=-114,2;CIEND95=-74,5;MATEID=2029_2;EVENT=2029;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:30:0:-3,-6,-25:31:28:2:28:2:0:0:0:28:2:0.067	0/1:56:56.6:-15,-9,-44:62:53:8:53:8:0:0:0:53:8:0.13
+3	105828859	2016_1	N	]5:141379626]N	9.54	.	SVTYPE=BND;STRANDS=-+:10;IMPRECISE;CIPOS=-339,29;CIEND=-30,223;CIPOS95=-117,3;CIEND95=-4,92;MATEID=2016_2;EVENT=2016;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:0:2.92:-5,-5,-24:31:27:3:27:3:0:0:0:27:3:0.1	0/1:5:6.63:-12,-11,-52:69:61:7:61:7:0:0:0:61:7:0.1
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+3	151748833	452_1	N	[3:176444683[N	128.49	.	SVTYPE=BND;STRANDS=--:14;IMPRECISE;CIPOS=-195,25;CIEND=-316,29;CIPOS95=-82,4;CIEND95=-107,2;MATEID=452_2;EVENT=452;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:144:0:-0,-14,-48:50:49:0:48:0:21:0:0:27:0:0	0/1:128:128.49:-22,-10,-52:78:65:12:65:12:0:0:0:65:12:0.16
+3	158034493	2019_1	N	N]6:32688592]	74.64	.	SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-30,336;CIEND=-30,259;CIPOS95=-2,119;CIEND95=-5,83;MATEID=2019_2;EVENT=2019;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:0:2.95:-4,-4,-16:21:18:2:18:2:0:0:0:18:2:0.1	0/1:71:71.7:-13,-6,-32:47:39:7:39:7:0:0:0:39:7:0.15
+3	176444683	452_2	N	[3:151748833[N	128.49	.	SVTYPE=BND;STRANDS=--:14;IMPRECISE;CIPOS=-316,29;CIEND=-195,25;CIPOS95=-107,2;CIEND95=-82,4;MATEID=452_1;EVENT=452;SECONDARY;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:144:0:-0,-14,-48:50:49:0:48:0:21:0:0:27:0:0	0/1:128:128.49:-22,-10,-52:78:65:12:65:12:0:0:0:65:12:0.16
+3	182298978	2028_1	N	N[11:94948981[	125.52	.	SVTYPE=BND;STRANDS=+-:15;IMPRECISE;CIPOS=-30,181;CIEND=-225,14;CIPOS95=-6,68;CIEND95=-114,2;MATEID=2028_2;EVENT=2028;SU=15;PE=15;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:0:2.92:-5,-5,-24:31:27:3:27:3:0:0:0:27:3:0.1	0/1:122:122.61:-19,-7,-39:60:49:10:49:10:0:0:0:49:10:0.17
+3	182299013	2024_1	N	N[9:1940734[	92.74	.	SVTYPE=BND;STRANDS=+-:8;IMPRECISE;CIPOS=-30,218;CIEND=-347,29;CIPOS95=-6,66;CIEND95=-133,1;MATEID=2024_2;EVENT=2024;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:69:0:-0,-7,-23:25:24:0:23:0:11:0:0:12:0:0	0/1:92:92.74:-14,-5,-25:40:32:7:32:7:0:0:0:32:7:0.18
+3	184156702	2039_1	N	N]20:231409]	74.64	.	SVTYPE=BND;STRANDS=++:7;IMPRECISE;CIPOS=-30,247;CIEND=-30,347;CIPOS95=-3,103;CIEND95=-1,138;MATEID=2039_2;EVENT=2039;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:144:0:-0,-14,-48:50:49:0:48:0:26:0:0:22:0:0	0/1:74:74.64:-15,-7,-38:56:47:8:47:8:0:0:0:47:8:0.15
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+3	192376521	2027_1	N	N]10:65545580]	77.58	.	SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-28,201;CIEND=-30,218;CIPOS95=-5,76;CIEND95=-2,97;MATEID=2027_2;EVENT=2027;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:120:0:-0,-12,-40:42:41:0:40:0:17:0:0:23:0:0	0/1:77:77.58:-17,-9,-45:65:55:9:55:9:0:0:0:55:9:0.14
+4	44842163	1942_2	N	]1:42552553]N	59.54	.	SVTYPE=BND;STRANDS=-+:7;IMPRECISE;CIPOS=-238,29;CIEND=-15,285;CIPOS95=-86,5;CIEND95=-1,137;MATEID=1942_1;EVENT=1942;SECONDARY;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:57:0:-3,-9,-34:40:37:2:37:2:0:0:0:37:2:0.051	0/1:59:59.54:-16,-10,-51:71:61:9:61:9:0:0:0:61:9:0.13
+4	68944782	1977_2	N	N]2:204273805]	62.68	.	SVTYPE=BND;STRANDS=++:6;IMPRECISE;CIPOS=-30,257;CIEND=-30,269;CIPOS95=-3,96;CIEND95=-4,116;MATEID=1977_1;EVENT=1977;SECONDARY;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:84:0:-0,-8,-28:30:29:0:28:0:15:0:0:13:0:0	0/1:62:62.68:-13,-7,-34:50:42:7:42:7:0:0:0:42:7:0.14
+4	73831211	526	N	<DEL>	50.02	.	SVTYPE=DEL;SVLEN=-607;END=73831818;STRANDS=+-:18;IMPRECISE;CIPOS=-24,181;CIEND=-193,23;CIPOS95=-5,72;CIEND95=-92,3;SU=18;PE=18;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:93:0:-6,-15,-61:73:68:4:67:4:34:0:1:33:3:0.056	0/1:50:50.02:-29,-24,-115:155:137:18:136:17:71:0:4:65:13:0.11
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+6	68923562	2046_2	N	]4:81136688]N	6.63	.	SVTYPE=BND;STRANDS=-+:8;IMPRECISE;CIPOS=-321,29;CIEND=-30,226;CIPOS95=-121,3;CIEND95=-5,93;MATEID=2046_1;EVENT=2046;SECONDARY;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:147:0:-0,-15,-49:50:50:0:49:0:20:0:0:29:0:0	0/1:5:6.63:-12,-11,-52:69:61:7:61:7:0:0:0:61:7:0.1
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+6	74156485	2110_1	N	N]14:71480241]	35.69	.	SVTYPE=BND;STRANDS=++:7;IMPRECISE;CIPOS=-30,265;CIEND=-30,239;CIPOS95=-3,121;CIEND95=-5,91;MATEID=2110_2;EVENT=2110;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:147:0:-0,-15,-49:50:50:0:49:0:24:0:0:25:0:0	0/1:35:35.69:-11,-7,-35:49:42:6:42:6:0:0:0:42:6:0.12
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+6	107307808	2100_1	N	N[8:105231718[	98.37	.	SVTYPE=BND;STRANDS=+-:17;IMPRECISE;CIPOS=-30,238;CIEND=-281,29;CIPOS95=-6,51;CIEND95=-89,3;MATEID=2100_2;EVENT=2100;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:84:0:-3,-11,-43:49:46:2:46:2:0:0:0:46:2:0.042	0/1:98:98.37:-23,-14,-69:98:84:13:84:13:0:0:0:84:13:0.13
+6	136589486	906	N	<DEL>	270.05	.	SVTYPE=DEL;SVLEN=-1088;END=136590574;STRANDS=+-:26;IMPRECISE;CIPOS=-20,157;CIEND=-290,29;CIPOS95=-2,67;CIEND95=-74,3;SU=26;PE=26;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:6:0.92:-7,-8,-33:43:38:4:38:4:0:0:0:38:4:0.095	0/1:200:269.13:-41,-14,-84:131:108:22:108:22:0:0:0:108:22:0.17
+6	159204434	1952_2	N	[1:64897140[N	35.75	.	SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-250,29;CIEND=-289,21;CIPOS95=-106,5;CIEND95=-137,3;MATEID=1952_1;EVENT=1952;SECONDARY;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:75:0:-0,-8,-25:27:26:0:25:0:9:0:0:16:0:0	0/1:35:35.75:-9,-6,-28:39:33:5:33:5:0:0:0:33:5:0.13
+6	161336425	2096_1	N	N[7:85956546[	77.71	.	SVTYPE=BND;STRANDS=+-:8;IMPRECISE;CIPOS=-30,264;CIEND=-252,29;CIPOS95=-4,113;CIEND95=-114,3;MATEID=2096_2;EVENT=2096;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:93:0:-0,-9,-31:32:32:0:31:0:16:0:0:15:0:0	0/1:77:77.71:-13,-6,-30:45:37:7:37:7:0:0:0:37:7:0.16
+7	8663298	2072_2	N	]5:37709852]N	23.36	.	SVTYPE=BND;STRANDS=-+:12;IMPRECISE;CIPOS=-187,29;CIEND=-23,233;CIPOS95=-65,3;CIEND95=-2,114;MATEID=2072_1;EVENT=2072;SECONDARY;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:93:0:-1,-11,-38:42:40:1:40:1:0:0:0:40:1:0.024	0/1:23:23.36:-19,-16,-77:103:91:11:91:11:0:0:0:91:11:0.11
+7	32225987	2020_2	N	N]3:48372309]	17.6	.	SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-21,243;CIEND=-30,202;CIPOS95=-3,120;CIEND95=-3,76;MATEID=2020_1;EVENT=2020;SECONDARY;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:63:0:-2,-8,-29:32:30:1:30:1:0:0:0:30:1:0.032	0/1:17:17.6:-14,-12,-56:75:66:8:66:8:0:0:0:66:8:0.11
+7	52399206	1982_2	N	N]2:12019022]	14.67	.	SVTYPE=BND;STRANDS=++:9;IMPRECISE;CIPOS=-19,261;CIEND=-30,221;CIPOS95=-2,131;CIEND95=-2,91;MATEID=1982_1;EVENT=1982;SECONDARY;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:0:-0,-24,-80:81:81:0:80:0:41:0:0:39:0:0	0/1:14:14.67:-14,-12,-57:76:67:8:67:8:0:0:0:67:8:0.11
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+7	68758443	2095_2	N	[6:26625483[N	71.63	.	SVTYPE=BND;STRANDS=--:9;IMPRECISE;CIPOS=-228,29;CIEND=-211,27;CIPOS95=-94,5;CIEND95=-91,5;MATEID=2095_1;EVENT=2095;SECONDARY;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:156:0:-0,-16,-52:54:53:0:52:0:22:0:0:30:0:0	0/1:71:71.63:-15,-8,-39:57:48:8:48:8:0:0:0:48:8:0.14
+7	70420972	968_1	N	N]7:70438890]	215.61	.	SVTYPE=BND;STRANDS=++:16;IMPRECISE;CIPOS=-30,218;CIEND=-30,162;CIPOS95=-7,56;CIEND95=-5,55;MATEID=968_2;EVENT=968;SU=16;PE=16;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-2,-4,-17:20:18:1:18:1:0:0:0:18:1:0.053	0/1:200:215.6:-27,-5,-33:59:45:13:45:13:0:0:0:45:13:0.22
+7	70438890	968_2	N	N]7:70420972]	215.61	.	SVTYPE=BND;STRANDS=++:16;IMPRECISE;CIPOS=-30,162;CIEND=-30,218;CIPOS95=-5,55;CIEND95=-7,56;MATEID=968_1;EVENT=968;SECONDARY;SU=16;PE=16;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-2,-4,-17:20:18:1:18:1:0:0:0:18:1:0.053	0/1:200:215.6:-27,-5,-33:59:45:13:45:13:0:0:0:45:13:0.22
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+7	93357413	1954_2	N	]1:105428633]N	104.7	.	SVTYPE=BND;STRANDS=-+:9;IMPRECISE;CIPOS=-225,29;CIEND=-21,258;CIPOS95=-93,4;CIEND95=-2,129;MATEID=1954_1;EVENT=1954;SECONDARY;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:102:0:-0,-10,-34:36:35:0:34:0:16:0:0:18:0:0	0/1:104:104.7:-16,-5,-29:46:37:8:37:8:0:0:0:37:8:0.18
+7	93541820	990	N	<DEL>	197.47	.	SVTYPE=DEL;SVLEN=-726;END=93542546;STRANDS=+-:18;IMPRECISE;CIPOS=-23,176;CIEND=-171,28;CIPOS95=-3,64;CIEND95=-61,5;SU=18;PE=18;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:0:2.92:-5,-5,-24:31:27:3:27:3:0:0:0:27:3:0.1	0/1:194:194.56:-26,-6,-39:66:52:13:52:13:0:0:0:52:13:0.2
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+7	156387226	1037_2	N	N]7:156387047]	111.08	.	SVTYPE=BND;STRANDS=++:14;IMPRECISE;CIPOS=-18,220;CIEND=-30,38;CIPOS95=-1,109;CIEND95=-3,38;MATEID=1037_1;EVENT=1037;SECONDARY;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.5:-4,-5,-19:24:21:2:21:2:0:0:0:21:2:0.087	0/1:110:110.58:-19,-8,-42:64:53:10:53:10:0:0:0:53:10:0.16
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+8	30145409	2157_1	N	]17:7167951]N	146.33	.	SVTYPE=BND;STRANDS=-+:12;IMPRECISE;CIPOS=-221,26;CIEND=-30,192;CIPOS95=-99,4;CIEND95=-6,76;MATEID=2157_2;EVENT=2157;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:84:0:-1,-10,-35:39:37:1:37:1:0:0:0:37:1:0.026	0/1:146:146.33:-28,-13,-69:102:86:15:86:15:0:0:0:86:15:0.15
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+8	75876952	2022_2	N	[3:38399708[N	69.39	.	SVTYPE=BND;STRANDS=--:7;IMPRECISE;CIPOS=-278,21;CIEND=-183,29;CIPOS95=-131,3;CIEND95=-61,8;MATEID=2022_1;EVENT=2022;SECONDARY;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.51:-2,-3,-11:14:12:1:12:1:0:0:0:12:1:0.077	0/1:68:68.88:-9,-2,-10:18:13:4:13:4:0:0:0:13:4:0.24
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+8	140475502	2147_1	N	N[11:56303340[	65.81	.	SVTYPE=BND;STRANDS=+-:6;IMPRECISE;CIPOS=-30,330;CIEND=-314,29;CIPOS95=-3,130;CIEND95=-123,3;MATEID=2147_2;EVENT=2147;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:81:0:-0,-8,-27:29:28:0:27:0:12:0:0:15:0:0	0/1:65:65.81:-10,-3,-18:29:23:5:23:5:0:0:0:23:5:0.18
+9	1940734	2024_2	N	]3:182299013]N	92.74	.	SVTYPE=BND;STRANDS=-+:8;IMPRECISE;CIPOS=-347,29;CIEND=-30,218;CIPOS95=-133,1;CIEND95=-6,66;MATEID=2024_1;EVENT=2024;SECONDARY;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:69:0:-0,-7,-23:25:24:0:23:0:11:0:0:12:0:0	0/1:92:92.74:-14,-5,-25:40:32:7:32:7:0:0:0:32:7:0.18
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+9	127885505	2170_1	N	N]18:71711520]	26.91	.	SVTYPE=BND;STRANDS=++:15;IMPRECISE;CIPOS=-30,297;CIEND=-30,276;CIPOS95=-4,85;CIEND95=-5,72;MATEID=2170_2;EVENT=2170;SU=15;PE=15;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.49:-7,-8,-34:44:39:4:39:4:0:0:0:39:4:0.093	0/1:26:26.42:-17,-15,-69:92:81:10:81:10:0:0:0:81:10:0.11
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+10	107209	2162_2	N	[9:141058509[N	65.36	.	SVTYPE=BND;STRANDS=--:14;IMPRECISE;CIPOS=-307,29;CIEND=-283,29;CIPOS95=-97,4;CIEND95=-88,2;MATEID=2162_1;EVENT=2162;SECONDARY;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:63:0:-2,-8,-29:32:30:1:30:1:0:0:0:30:1:0.032	0/1:65:65.36:-21,-15,-72:99:86:12:86:12:0:0:0:86:12:0.12
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+10	68673027	2174_1	N	N]16:59976476]	26.5	.	SVTYPE=BND;STRANDS=++:15;IMPRECISE;CIPOS=-30,194;CIEND=-30,168;CIPOS95=-7,54;CIEND95=-6,53;MATEID=2174_2;EVENT=2174;SU=15;PE=15;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:24:0.02:-7,-9,-39:49:44:4:44:4:0:0:0:44:4:0.083	0/1:26:26.49:-16,-13,-61:82:72:9:72:9:0:0:0:72:9:0.11
+10	75489000	2075_2	N	]5:54865801]N	192.34	.	SVTYPE=BND;STRANDS=-+:20;IMPRECISE;CIPOS=-204,12;CIEND=-30,152;CIPOS95=-104,1;CIEND95=-6,52;MATEID=2075_1;EVENT=2075;SECONDARY;SU=20;PE=20;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:6:0.92:-7,-8,-33:43:38:4:38:4:0:0:0:38:4:0.095	0/1:191:191.42:-29,-10,-55:87:71:15:71:15:0:0:0:71:15:0.17
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+10	123120353	2057_2	N	]4:175534267]N	44.64	.	SVTYPE=BND;STRANDS=-+:9;IMPRECISE;CIPOS=-334,29;CIEND=-30,221;CIPOS95=-128,1;CIEND95=-6,88;MATEID=2057_1;EVENT=2057;SECONDARY;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:111:0:-0,-11,-37:39:38:0:37:0:15:0:0:22:0:0	0/1:44:44.64:-13,-8,-40:56:48:7:48:7:0:0:0:48:7:0.13
+10	132635667	1304_1	N	N]10:132636051]	170.7	.	SVTYPE=BND;STRANDS=++:13;IMPRECISE;CIPOS=-30,150;CIEND=-30,227;CIPOS95=-6,74;CIEND95=-3,66;MATEID=1304_2;EVENT=1304;SU=13;PE=13;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:30:0:-2,-5,-18:21:19:1:19:1:0:0:0:19:1:0.05	0/1:170:170.7:-21,-4,-24:44:33:10:33:10:0:0:0:33:10:0.23
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+14	63226299	1586_2	N	N]14:47118175]	350.61	.	SVTYPE=BND;STRANDS=++:20;IMPRECISE;CIPOS=-30,155;CIEND=-30,172;CIPOS95=-4,53;CIEND95=-4,77;MATEID=1586_1;EVENT=1586;SECONDARY;SU=20;PE=20;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:30:0:-2,-5,-18:21:19:1:19:1:0:0:0:19:1:0.05	0/1:200:350.61:-38,-2,-23:54:36:17:36:17:0:0:0:36:17:0.32
+14	65842539	1590_1	N	N]14:65843134]	290.56	.	SVTYPE=BND;STRANDS=++:18;IMPRECISE;CIPOS=-25,172;CIEND=-28,158;CIPOS95=-3,64;CIEND95=-4,52;MATEID=1590_2;EVENT=1590;SU=18;PE=18;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:120:0:-0,-12,-40:42:41:0:40:0:20:0:0:20:0:0	0/1:200:290.56:-33,-4,-33:64:47:16:47:16:0:0:0:47:16:0.25
+14	65843134	1590_2	N	N]14:65842539]	290.56	.	SVTYPE=BND;STRANDS=++:18;IMPRECISE;CIPOS=-28,158;CIEND=-25,172;CIPOS95=-4,52;CIEND95=-3,64;MATEID=1590_1;EVENT=1590;SECONDARY;SU=18;PE=18;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:120:0:-0,-12,-40:42:41:0:40:0:20:0:0:20:0:0	0/1:200:290.56:-33,-4,-33:64:47:16:47:16:0:0:0:47:16:0.25
+14	71480241	2110_2	N	N]6:74156485]	35.69	.	SVTYPE=BND;STRANDS=++:7;IMPRECISE;CIPOS=-30,239;CIEND=-30,265;CIPOS95=-5,91;CIEND95=-3,121;MATEID=2110_1;EVENT=2110;SECONDARY;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:147:0:-0,-15,-49:50:50:0:49:0:24:0:0:25:0:0	0/1:35:35.69:-11,-7,-35:49:42:6:42:6:0:0:0:42:6:0.12
+14	80106294	1596	N	<DEL>	362.16	.	SVTYPE=DEL;SVLEN=-8751;END=80115045;STRANDS=+-:22;IMPRECISE;CIPOS=-26,145;CIEND=-169,29;CIPOS95=-3,49;CIEND95=-45,8;SU=22;PE=22;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:0:2.85:-9,-9,-39:52:46:5:45:5:23:0:2:22:3:0.1	0/1:200:359.31:-44,-8,-57:102:79:22:78:22:39:0:4:39:18:0.22
+14	90299534	1604_1	N	N]14:90302487]	305.41	.	SVTYPE=BND;STRANDS=++:24;IMPRECISE;CIPOS=-24,172;CIEND=-28,149;CIPOS95=-2,80;CIEND95=-5,56;MATEID=1604_2;EVENT=1604;SU=24;PE=24;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:24:0.02:-5,-8,-31:39:35:3:35:3:0:0:0:35:3:0.079	0/1:200:305.39:-38,-8,-51:89:69:19:69:19:0:0:0:69:19:0.22
+14	90302487	1604_2	N	N]14:90299534]	305.41	.	SVTYPE=BND;STRANDS=++:24;IMPRECISE;CIPOS=-28,149;CIEND=-24,172;CIPOS95=-5,56;CIEND95=-2,80;MATEID=1604_1;EVENT=1604;SECONDARY;SU=24;PE=24;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:24:0.02:-5,-8,-31:39:35:3:35:3:0:0:0:35:3:0.079	0/1:200:305.39:-38,-8,-51:89:69:19:69:19:0:0:0:69:19:0.22
+14	106484224	2198_1	N	N[15:22486809[	32.3	.	SVTYPE=BND;STRANDS=+-:18;IMPRECISE;CIPOS=-19,183;CIEND=-170,19;CIPOS95=-3,77;CIEND95=-57,2;MATEID=2198_2;EVENT=2198;SU=18;PE=18;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:36:0:-7,-10,-43:53:48:4:48:4:0:0:0:48:4:0.077	0/1:32:32.3:-21,-17,-82:110:97:12:97:12:0:0:0:97:12:0.11
+15	22486809	2198_2	N	]14:106484224]N	32.3	.	SVTYPE=BND;STRANDS=-+:18;IMPRECISE;CIPOS=-170,19;CIEND=-19,183;CIPOS95=-57,2;CIEND95=-3,77;MATEID=2198_1;EVENT=2198;SECONDARY;SU=18;PE=18;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:36:0:-7,-10,-43:53:48:4:48:4:0:0:0:48:4:0.077	0/1:32:32.3:-21,-17,-82:110:97:12:97:12:0:0:0:97:12:0.11
+15	39744398	1623	N	<DEL>	242.33	.	SVTYPE=DEL;SVLEN=-451;END=39744849;STRANDS=+-:18;IMPRECISE;CIPOS=-19,199;CIEND=-178,29;CIPOS95=-2,84;CIEND95=-35,7;SU=18;PE=18;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:18:0.06:-8,-10,-45:58:52:6:51:5:27:0:1:24:4:0.089	0/1:200:242.27:-36,-12,-70:112:91:20:90:19:44:0:6:46:13:0.17
+15	51189306	1963_2	N	]1:119401195]N	41.32	.	SVTYPE=BND;STRANDS=-+:14;IMPRECISE;CIPOS=-192,29;CIEND=-30,271;CIPOS95=-71,6;CIEND95=-3,87;MATEID=1963_1;EVENT=1963;SECONDARY;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:60:0:-5,-11,-43:51:47:3:47:3:0:0:0:47:3:0.06	0/1:41:41.32:-21,-17,-79:107:94:12:94:12:0:0:0:94:12:0.11
+15	52589534	2087_2	N	N]5:5595231]	45.28	.	SVTYPE=BND;STRANDS=++:8;IMPRECISE;CIPOS=-30,339;CIEND=-30,176;CIPOS95=-2,128;CIEND95=-8,51;MATEID=2087_1;EVENT=2087;SECONDARY;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.51:-2,-3,-11:14:12:1:12:1:0:0:0:12:1:0.077	0/1:44:44.77:-10,-5,-25:36:30:5:30:5:0:0:0:30:5:0.14
+15	62706095	1637	N	<DEL>	170.38	.	SVTYPE=DEL;SVLEN=-1686;END=62707781;STRANDS=+-:15;IMPRECISE;CIPOS=-30,148;CIEND=-194,29;CIPOS95=-8,44;CIEND95=-85,4;SU=15;PE=15;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:108:0:-3,-14,-51:59:55:3:54:2:27:0:0:27:2:0.036	0/1:170:170.38:-28,-11,-62:95:79:16:78:15:35:0:3:43:12:0.16
+15	75867566	2201_1	N	N]16:89281701]	110.58	.	SVTYPE=BND;STRANDS=++:12;IMPRECISE;CIPOS=-25,222;CIEND=-30,224;CIPOS95=-3,102;CIEND95=-5,81;MATEID=2201_2;EVENT=2201;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:180:0:-0,-18,-60:62:61:0:60:0:29:0:0:31:0:0	0/1:110:110.58:-19,-8,-42:64:53:10:53:10:0:0:0:53:10:0.16
+16	3354097	2156_2	N	N]8:59616000]	4.43	.	SVTYPE=BND;STRANDS=++:10;IMPRECISE;CIPOS=-16,247;CIEND=-30,246;CIPOS95=-1,117;CIEND95=-5,81;MATEID=2156_1;EVENT=2156;SECONDARY;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:159:0:-0,-16,-53:55:54:0:53:0:27:0:0:26:0:0	0/1:2:4.43:-14,-13,-61:80:71:8:71:8:0:0:0:71:8:0.1
+16	13294470	1665	N	<DEL>	209.2	.	SVTYPE=DEL;SVLEN=-2020;END=13296490;STRANDS=+-:17;IMPRECISE;CIPOS=-30,183;CIEND=-181,29;CIPOS95=-4,82;CIEND95=-40,9;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:33:0:-7,-10,-42:53:48:5:47:4:22:0:3:25:1:0.078	0/1:200:209.2:-35,-14,-80:122:102:19:101:19:48:0:4:53:15:0.16
+16	33485944	1674	N	<DEL>	116.47	.	SVTYPE=DEL;SVLEN=-336;END=33486280;STRANDS=+-:10;IMPRECISE;CIPOS=-30,268;CIEND=-264,29;CIPOS95=-4,81;CIEND95=-84,5;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:18:0.06:-7,-9,-37:47:42:4:42:4:0:0:0:42:4:0.087	0/1:116:116.4:-24,-12,-63:92:78:13:78:13:0:0:0:78:13:0.14
+16	59323740	1969_2	N	]1:234805693]N	20.7	.	SVTYPE=BND;STRANDS=-+:7;IMPRECISE;CIPOS=-347,29;CIEND=-30,282;CIPOS95=-138,1;CIEND95=-4,98;MATEID=1969_1;EVENT=1969;SECONDARY;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:138:0:-0,-14,-46:47:47:0:46:0:24:0:0:22:0:0	0/1:20:20.7:-11,-9,-40:54:47:6:47:6:0:0:0:47:6:0.11
+16	59976476	2174_2	N	N]10:68673027]	26.5	.	SVTYPE=BND;STRANDS=++:15;IMPRECISE;CIPOS=-30,168;CIEND=-30,194;CIPOS95=-6,53;CIEND95=-7,54;MATEID=2174_1;EVENT=2174;SECONDARY;SU=15;PE=15;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:24:0.02:-7,-9,-39:49:44:4:44:4:0:0:0:44:4:0.083	0/1:26:26.49:-16,-13,-61:82:72:9:72:9:0:0:0:72:9:0.11
+16	69854786	1684	N	<DUP>	17.22	.	SVTYPE=DUP;SVLEN=4240;END=69859026;STRANDS=-+:9;IMPRECISE;CIPOS=-312,29;CIEND=-24,234;CIPOS95=-109,3;CIEND95=-2,98;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:16:0.09:-1,-2,-5:34:32:1:32:1:0:0:0:32:1:0.03	0/1:17:17.12:-5,-3,-8:88:80:7:80:7:0:0:0:80:7:0.08
+16	76865795	2140_2	N	N[7:127930431[	138.22	.	SVTYPE=BND;STRANDS=+-:20;IMPRECISE;CIPOS=-30,160;CIEND=-179,18;CIPOS95=-5,57;CIEND95=-67,4;MATEID=2140_1;EVENT=2140;SECONDARY;SU=20;PE=20;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:6:0.91:-9,-9,-41:53:47:5:47:5:0:0:0:47:5:0.096	0/1:137:137.32:-27,-14,-72:105:89:15:89:15:0:0:0:89:15:0.14
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+16	89281701	2201_2	N	N]15:75867566]	110.58	.	SVTYPE=BND;STRANDS=++:12;IMPRECISE;CIPOS=-30,224;CIEND=-25,222;CIPOS95=-5,81;CIEND95=-3,102;MATEID=2201_1;EVENT=2201;SECONDARY;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:180:0:-0,-18,-60:62:61:0:60:0:29:0:0:31:0:0	0/1:110:110.58:-19,-8,-42:64:53:10:53:10:0:0:0:53:10:0.16
+17	7167951	2157_2	N	N[8:30145409[	146.33	.	SVTYPE=BND;STRANDS=+-:12;IMPRECISE;CIPOS=-30,192;CIEND=-221,26;CIPOS95=-6,76;CIEND95=-99,4;MATEID=2157_1;EVENT=2157;SECONDARY;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:84:0:-1,-10,-35:39:37:1:37:1:0:0:0:37:1:0.026	0/1:146:146.33:-28,-13,-69:102:86:15:86:15:0:0:0:86:15:0.15
+17	45634774	1714	N	<DEL>	135.29	.	SVTYPE=DEL;SVLEN=-510;END=45635284;STRANDS=+-:12;IMPRECISE;CIPOS=-20,235;CIEND=-234,29;CIPOS95=-2,114;CIEND95=-59,6;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:6:0.92:-7,-8,-33:44:39:4:38:4:17:0:3:21:1:0.095	0/1:134:134.37:-26,-12,-65:97:82:14:81:14:41:0:5:40:9:0.15
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+17	70815221	1725	N	<DEL>	134.65	.	SVTYPE=DEL;SVLEN=-6134;END=70821355;STRANDS=+-:14;IMPRECISE;CIPOS=-27,177;CIEND=-217,29;CIPOS95=-4,61;CIEND95=-42,7;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:24:0.02:-3,-6,-24:29:26:2:26:2:0:0:0:26:2:0.071	0/1:134:134.63:-20,-6,-35:56:45:10:45:10:0:0:0:45:10:0.18
+17	74377266	2002_2	N	]2:153997618]N	23.44	.	SVTYPE=BND;STRANDS=-+:14;IMPRECISE;CIPOS=-220,20;CIEND=-30,176;CIPOS95=-101,2;CIEND95=-6,60;MATEID=2002_1;EVENT=2002;SECONDARY;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-5,-8,-32:40:36:3:36:3:0:0:0:36:3:0.077	0/1:23:23.43:-17,-15,-70:93:82:10:82:10:0:0:0:82:10:0.11
+18	39585688	1754	N	<DEL>	155.16	.	SVTYPE=DEL;SVLEN=-625;END=39586313;STRANDS=+-:17;IMPRECISE;CIPOS=-30,251;CIEND=-263,29;CIPOS95=-3,64;CIEND95=-63,6;SU=17;PE=17;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:63:0:-5,-11,-44:54:49:4:48:3:21:0:2:27:1:0.059	0/1:155:155.16:-32,-17,-89:131:111:19:110:18:52:0:4:58:14:0.14
+18	59713754	2004_2	N	]2:77358259]N	4.44	.	SVTYPE=BND;STRANDS=-+:11;IMPRECISE;CIPOS=-216,28;CIEND=-19,255;CIPOS95=-83,4;CIEND95=-3,122;MATEID=2004_1;EVENT=2004;SECONDARY;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-3,-6,-24:30:27:2:27:2:0:0:0:27:2:0.069	0/1:2:4.43:-14,-13,-61:80:71:8:71:8:0:0:0:71:8:0.1
+18	71711520	2170_2	N	N]9:127885505]	26.91	.	SVTYPE=BND;STRANDS=++:15;IMPRECISE;CIPOS=-30,276;CIEND=-30,297;CIPOS95=-5,72;CIEND95=-4,85;MATEID=2170_1;EVENT=2170;SECONDARY;SU=15;PE=15;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.49:-7,-8,-34:44:39:4:39:4:0:0:0:39:4:0.093	0/1:26:26.42:-17,-15,-69:92:81:10:81:10:0:0:0:81:10:0.11
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+19	15046341	1793	N	<DEL>	170.94	.	SVTYPE=DEL;SVLEN=-3130;END=15049471;STRANDS=+-:19;IMPRECISE;CIPOS=-25,174;CIEND=-189,20;CIPOS95=-4,71;CIEND95=-84,3;SU=19;PE=19;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:9:0.49:-5,-6,-26:34:30:3:30:3:0:0:0:30:3:0.091	0/1:170:170.44:-27,-10,-54:84:69:14:69:14:0:0:0:69:14:0.17
+19	18835613	2159_2	N	N[8:96265720[	9.02	.	SVTYPE=BND;STRANDS=+-:12;IMPRECISE;CIPOS=-30,232;CIEND=-252,29;CIPOS95=-6,64;CIEND95=-81,4;MATEID=2159_1;EVENT=2159;SECONDARY;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:51:0:-3,-8,-32:38:35:2:35:2:0:0:0:35:2:0.054	0/1:8:9.02:-15,-14,-67:88:78:9:78:9:0:0:0:78:9:0.1
+19	24027918	1971_2	N	N]1:28515659]	194.49	.	SVTYPE=BND;STRANDS=++:12;IMPRECISE;CIPOS=-30,228;CIEND=-24,212;CIPOS95=-4,73;CIEND95=-4,93;MATEID=1971_1;EVENT=1971;SECONDARY;SU=12;PE=12;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:162:0:-0,-16,-54:56:55:0:54:0:23:0:0:31:0:0	0/1:194:194.49:-27,-8,-47:76:61:14:61:14:0:0:0:61:14:0.19
+19	24033135	1972_2	N	N[1:168024578[	4.57	.	SVTYPE=BND;STRANDS=+-:8;IMPRECISE;CIPOS=-30,210;CIEND=-274,18;CIPOS95=-6,75;CIEND95=-129,2;MATEID=1972_1;EVENT=1972;SECONDARY;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-2,-4,-17:20:18:1:18:1:0:0:0:18:1:0.053	0/1:2:4.56:-9,-8,-38:50:44:5:44:5:0:0:0:44:5:0.1
+19	51077891	1805	N	<DEL>	68.37	.	SVTYPE=DEL;SVLEN=-4630;END=51082521;STRANDS=+-:11;IMPRECISE;CIPOS=-30,317;CIEND=-217,29;CIPOS95=-4,104;CIEND95=-93,4;SU=11;PE=11;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:60:0:-3,-9,-35:42:39:3:38:2:18:0:1:20:1:0.05	0/1:68:68.37:-21,-14,-71:99:86:12:85:12:45:0:4:40:8:0.12
+19	52567370	2007_2	N	[2:178351450[N	56.6	.	SVTYPE=BND;STRANDS=--:10;IMPRECISE;CIPOS=-244,28;CIEND=-283,29;CIPOS95=-104,2;CIEND95=-100,4;MATEID=2007_1;EVENT=2007;SECONDARY;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:45:0:-2,-6,-23:26:24:1:24:1:0:0:0:24:1:0.04	0/1:56:56.6:-15,-9,-44:62:53:8:53:8:0:0:0:53:8:0.13
+19	52567638	2006_2	N	N]2:178351470]	110.71	.	SVTYPE=BND;STRANDS=++:10;IMPRECISE;CIPOS=-30,187;CIEND=-30,147;CIPOS95=-6,54;CIEND95=-4,36;MATEID=2006_1;EVENT=2006;SECONDARY;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:84:0:-0,-8,-28:30:29:0:28:0:11:0:0:17:0:0	0/1:110:110.71:-16,-5,-27:44:35:8:35:8:0:0:0:35:8:0.19
+20	231409	2039_2	N	N]3:184156702]	74.64	.	SVTYPE=BND;STRANDS=++:7;IMPRECISE;CIPOS=-30,347;CIEND=-30,247;CIPOS95=-1,138;CIEND95=-3,103;MATEID=2039_1;EVENT=2039;SECONDARY;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:144:0:-0,-14,-48:50:49:0:48:0:26:0:0:22:0:0	0/1:74:74.64:-15,-7,-38:56:47:8:47:8:0:0:0:47:8:0.15
+20	3821170	1819	N	<DEL>	65.56	.	SVTYPE=DEL;SVLEN=-3950;END=3825120;STRANDS=+-:13;IMPRECISE;CIPOS=-30,160;CIEND=-326,29;CIPOS95=-7,48;CIEND95=-114,2;SU=13;PE=13;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:129:0:-3,-16,-58:65:62:3:61:2:29:0:0:32:2:0.032	0/1:65:65.56:-16,-10,-49:69:59:9:59:9:0:0:0:59:9:0.13
+20	61724700	1849	N	<DEL>	22.16	.	SVTYPE=DEL;SVLEN=-914;END=61725614;STRANDS=+-:8;IMPRECISE;CIPOS=-30,221;CIEND=-259,29;CIPOS95=-3,75;CIEND95=-76,6;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:3:1.72:-4,-4,-17:22:19:2:19:2:0:0:0:19:2:0.095	0/1:20:20.44:-17,-15,-71:96:84:11:83:10:39:0:2:44:8:0.11
+20	62949719	1851	N	<DEL>	140.64	.	SVTYPE=DEL;SVLEN=-9483;END=62959202;STRANDS=+-:14;IMPRECISE;CIPOS=-25,182;CIEND=-220,17;CIPOS95=-4,57;CIEND95=-103,3;SU=14;PE=14;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:48:0:-5,-10,-39:49:44:4:43:3:22:0:0:21:3:0.065	0/1:140:140.64:-20,-6,-33:54:43:10:43:10:0:0:0:43:10:0.19
+21	32956225	2215_1	N	]X:47183861]N	46.49	.	SVTYPE=BND;STRANDS=-+:8;IMPRECISE;CIPOS=-256,29;CIEND=-30,208;CIPOS95=-114,2;CIEND95=-3,74;MATEID=2215_2;EVENT=2215;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:3:1.72:-4,-4,-17:22:19:2:19:2:0:0:0:19:2:0.095	0/1:44:44.77:-10,-5,-25:36:30:5:30:5:0:0:0:30:5:0.14
+22	17770355	1872	N	<DEL>	295.13	.	SVTYPE=DEL;SVLEN=-8795;END=17779150;STRANDS=+-:22;IMPRECISE;CIPOS=-30,256;CIEND=-223,29;CIPOS95=-2,68;CIEND95=-58,6;SU=22;PE=22;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:3:1.7:-5,-6,-24:32:28:3:28:3:0:0:0:28:3:0.097	0/1:200:293.43:-36,-7,-47:82:64:18:64:18:0:0:0:64:18:0.22
+22	19099927	1874	N	<DEL>	4.31	.	SVTYPE=DEL;SVLEN=-694;END=19100621;STRANDS=+-:9;IMPRECISE;CIPOS=-24,167;CIEND=-195,29;CIPOS95=-7,61;CIEND95=-50,4;SU=9;PE=9;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:51:0:-5,-10,-40:50:45:4:44:3:22:0:2:22:1:0.064	0/1:2:4.31:-18,-18,-84:112:99:12:98:11:47:0:5:51:6:0.1
+X	3599701	2066_2	N	[4:162642267[N	44.77	.	SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-241,29;CIEND=-284,26;CIPOS95=-100,4;CIEND95=-130,1;MATEID=2066_1;EVENT=2066;SECONDARY;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:33:0:-0,-3,-11:12:12:0:11:0:4:0:0:7:0:0	0/1:44:44.77:-10,-5,-25:36:30:5:30:5:0:0:0:30:5:0.14
+X	3599706	2067_2	N	N]4:162642407]	50.72	.	SVTYPE=BND;STRANDS=++:7;IMPRECISE;CIPOS=-30,243;CIEND=-27,268;CIPOS95=-4,105;CIEND95=-3,127;MATEID=2067_1;EVENT=2067;SECONDARY;SU=7;PE=7;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:45:0:-0,-5,-15:17:16:0:15:0:5:0:0:10:0:0	0/1:50:50.72:-11,-6,-30:44:37:6:37:6:0:0:0:37:6:0.14
+X	11952984	2197_2	N	]13:35787786]N	50.53	.	SVTYPE=BND;STRANDS=-+:10;IMPRECISE;CIPOS=-257,16;CIEND=-30,224;CIPOS95=-129,2;CIEND95=-6,59;MATEID=2197_1;EVENT=2197;SECONDARY;SU=10;PE=10;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:0:-0,-20,-67:68:68:0:67:0:32:0:0:35:0:0	0/1:50:50.53:-16,-11,-53:74:64:9:64:9:0:0:0:64:9:0.12
+X	47183861	2215_2	N	N[21:32956225[	46.49	.	SVTYPE=BND;STRANDS=+-:8;IMPRECISE;CIPOS=-30,208;CIEND=-256,29;CIPOS95=-3,74;CIEND95=-114,2;MATEID=2215_1;EVENT=2215;SECONDARY;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:3:1.72:-4,-4,-17:22:19:2:19:2:0:0:0:19:2:0.095	0/1:44:44.77:-10,-5,-25:36:30:5:30:5:0:0:0:30:5:0.14
+X	55702382	1903	N	<DEL>	179.79	.	SVTYPE=DEL;SVLEN=-7503;END=55709885;STRANDS=+-:6;IMPRECISE;CIPOS=-30,263;CIEND=-286,29;CIPOS95=-2,105;CIEND95=-132,3;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:27:0.01:-2,-4,-17:21:19:1:18:1:8:0:1:10:0:0.053	0/1:123:179.78:-20,-2,-14:32:22:9:21:9:9:0:5:12:4:0.3
+X	114216686	1921_1	N	[X:114544524[N	11.1	.	SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-291,22;CIEND=-226,29;CIPOS95=-135,3;CIEND95=-85,6;MATEID=1921_2;EVENT=1921;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:3:1.74:-2,-2,-9:12:10:1:10:1:0:0:0:10:1:0.091	0/1:8:9.36:-6,-5,-21:28:24:3:24:3:0:0:0:24:3:0.11
+X	114544524	1921_2	N	[X:114216686[N	11.1	.	SVTYPE=BND;STRANDS=--:6;IMPRECISE;CIPOS=-226,29;CIEND=-291,22;CIPOS95=-85,6;CIEND95=-135,3;MATEID=1921_1;EVENT=1921;SECONDARY;SU=6;PE=6;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:3:1.74:-2,-2,-9:12:10:1:10:1:0:0:0:10:1:0.091	0/1:8:9.36:-6,-5,-21:28:24:3:24:3:0:0:0:24:3:0.11
+X	117432517	2119_2	N	N]6:17608998]	149.47	.	SVTYPE=BND;STRANDS=++:8;IMPRECISE;CIPOS=-30,284;CIEND=-30,301;CIPOS95=-3,108;CIEND95=-1,101;MATEID=2119_1;EVENT=2119;SECONDARY;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:0:-0,-27,-89:91:90:0:89:0:50:0:0:39:0:0	0/1:149:149.47:-25,-10,-53:81:67:13:67:13:0:0:0:67:13:0.16
+X	136092975	2142_2	N	]7:98015910]N	41.64	.	SVTYPE=BND;STRANDS=-+:8;IMPRECISE;CIPOS=-279,29;CIEND=-30,341;CIPOS95=-91,4;CIEND95=-1,133;MATEID=2142_1;EVENT=2142;SECONDARY;SU=8;PE=8;SR=0;AC=1;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:111:0:-0,-11,-37:38:38:0:37:0:17:0:0:20:0:0	0/1:41:41.64:-13,-8,-41:57:49:7:49:7:0:0:0:49:7:0.12
diff -r bd4135caa3fa -r ad8853ee9909 vcf2hrdetect.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2hrdetect.py	Sun Feb 14 23:59:42 2021 +0000
@@ -0,0 +1,41 @@
+import sys
+
+handle = open(sys.argv[1], 'r')
+vcfdict = dict()
+tabdict = dict()
+for line in handle:
+    if line[0] == "#":
+        continue
+    else:
+        tabline = line[:-1].split("\t")
+        vcfdict[tabline[2]] = tabline
+for id in vcfdict.keys():
+    if "_1" in id:
+        newid = id[:-2]
+        pointbreak = vcfdict[id][4]
+        if "]" in pointbreak:
+            coordbreak = pointbreak.split("]")[1].split(":")[1]
+            chrom = pointbreak.split("]")[1].split(":")[0]
+        elif "[" in pointbreak:
+            coordbreak = pointbreak.split("[")[1].split(":")[1]
+            chrom = pointbreak.split("[")[1].split(":")[0]
+        if vcfdict[id][0] == chrom:
+            tabdict[newid] = [chrom, vcfdict[id][1], chrom, coordbreak, "INV"]
+        else:
+            tabdict[newid] = [vcfdict[id][0], vcfdict[id][1],
+                              chrom, coordbreak, "TRA"]
+for id in list(vcfdict):
+    if "_" in id:
+        del(vcfdict[id])
+for id in vcfdict.keys():  # only sv that are not of type TRA or INV
+    chr1 = vcfdict[id][0]
+    chr2 = vcfdict[id][0]
+    pos1 = vcfdict[id][1]
+    pos2 = vcfdict[id][7].split("END=")[1].split(";")[0]
+    type = vcfdict[id][7].split("SVTYPE=")[1].split(";")[0]
+    tabdict[id] = [chr1, pos1, chr2, pos2, type]
+out = open(sys.argv[2], 'w')
+out.write("chr1\tpos1\tchr2\tpos2\ttype\n")
+for key in tabdict:
+    line = "\t".join(tabdict[key]) + "\n"
+    out.write(line)
diff -r bd4135caa3fa -r ad8853ee9909 vcf2hrdetect.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2hrdetect.xml	Sun Feb 14 23:59:42 2021 +0000
@@ -0,0 +1,35 @@
+<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1">
+    <description>to tabular hrdetect</description>
+    <macros>
+        <import>macro_lumpy_smoove.xml</import>
+    </macros>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+    @pipefail@
+    python '$__tool_directory__'/vcf2hrdetect.py '$lumpy_smoove_vcf' '$hrdetect_tabular'
+    ]]></command>
+    <inputs>
+        <param name="lumpy_smoove_vcf" type="data" format="vcf" label="lumpy-smoove vcf to process"/>
+   </inputs>
+
+    <outputs>
+        <data format="tabular" name="hrdetect_tabular" label="tabular hrdetec SVs" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" />
+            <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+**vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with
+the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv)
+    </help>
+
+    <citations>
+    <citation type="doi">10.1038/nm.4292</citation>
+  </citations>
+</tool>