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Added test data
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‎.gitignore

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/__pycache__/
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*.pyc
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*.pyo
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*.vcf
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*.vcf.gz
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*.vcf.gz.tbi
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/*.vcf
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/*.vcf.gz
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/*.vcf.gz.tbi
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/*.rp
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/*.rpdb
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/.*/
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/*.sh
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/test/actual_output.vcf

‎README.md

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where input is a list of tabix indexed+bgzipped VCF files and chromosomes are the chromosomes to merge. For further details see the help page:
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```
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```sh
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python3 svimmer -h
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```
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## Test data example
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```sh
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python3 svimmer test_vcfs chr20 > test/actual_output.vcf
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diff test/actual_output.vcf test/expected_output.vcf
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```
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## License
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GNU GPLv3

‎test/HG002_30x_Manta_v1.6.0_test_data.vcf.gz

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‎test/HG002_30x_Manta_v1.6.0_test_data.vcf.gz.tbi

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‎test/HG003_30x_Manta_v1.6.0_test_data.vcf.gz

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‎test/expected_output.vcf

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##fileformat=VCFv4.1
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##fileDate=20210107
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##contig=<ID=chr20,length=64444167>
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##INFO=<ID=NUM_MERGED_SVS,Number=1,Type=Integer,Description="Number of merged SVs.">
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##INFO=<ID=STDDEV_POS,Number=2,Type=Integer,Description="Std. dev of begin and end positions.">
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr20 41196482 . T TTATAAATATATATTATATATAATATATATTTATATAAATATATATTATATATAAATATATATTATATATAATATATATTTATATAAATATATATTATATATTATATAAATATTATATATAATATATATTTA 0 . END=41196482;SVTYPE=INS;SVLEN=131;CIGAR=1M131I;CIPOS=0,20;HOMLEN=20;HOMSEQ=TATAAATATATATTATATAT;NUM_MERGED_SVS=3;STDDEV_POS=0.00,0.00
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chr20 41257715 . AATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGACTACAGGCACACGCCACCATGCCTGGCTAAGTTTTCGTATTTTTAGTAGAGACGGGGTTTCACCATGCTAGCCAGGCTGGTCTCGAACTCCTGACCTTGTGATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTTAGCCACCACGCCCAACCCTTTTTTTTTTTGAGACGGAGTTTTGCTCTTGTCAGCCAGGCTGGGGTACAGTGGCACAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTG A 0 . END=41258003;SVTYPE=DEL;SVLEN=-288;CIGAR=1M288D;CIPOS=0,9;HOMLEN=9;HOMSEQ=ATTCTCCTG;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 41277701 . C <DEL> 0 . END=41278993;SVTYPE=DEL;SVLEN=-1292;IMPRECISE;CIPOS=-393,393;CIEND=-511,511;NUM_MERGED_SVS=3;STDDEV_POS=12.49,71.07
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chr20 41694772 . A AATGTCAAATTGCGATAAATAGAACACCCCCACCCCCAGGATGCTACTAGAGAGAATAATGGAGGAAAATTGATACATTAGATTAGAATAAT 0 . END=41694772;SVTYPE=INS;SVLEN=91;CIGAR=1M91I;CIPOS=0,46;HOMLEN=46;HOMSEQ=ATGTCAAATTGCGATAAATAGAACACCCCCACCCCCAGGATGCTAC;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 41912429 . AACTTCCACCTCCCGGGTTCAAGCAATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGG A 0 . END=41912485;SVTYPE=DEL;SVLEN=-56;CIGAR=1M56D;CIPOS=0,3;HOMLEN=3;HOMSEQ=ACT;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 42213265 . G GTTTCACATCATTAAAAGTTGTAGAATCTTGGATTCTCTGGCTGGAAAGGCCCTCCCA 0 . END=42213265;SVTYPE=INS;SVLEN=57;CIGAR=1M57I;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 42633975 . ATATTATATATTATATTATATATATTATATATATATAATATATATATAATATATATATTATATATATTATATATATATTATAAATATATAATATATATATAATATAT A 0 . END=42634081;SVTYPE=DEL;SVLEN=-106;CIGAR=1M106D;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 43162622 . TCTCCATGGTCCATCACTCTGGAGGCAGCAAGGAGTCAAGCTTCCAGGATCTGGTCTGGGGCTGCCTGGCTCCCCTTCCCTTCAGCCACACCAGTCAGTCACCCATGGTTCCAACCACACCAAAGGGTTTGGCTTTTCATGATGACCCGCTGGACAGCAGCTTGGCTCAGGCTGCTCTTCTGTCTG T 0 . END=43162807;SVTYPE=DEL;SVLEN=-185;CIGAR=1M185D;CIPOS=0,4;HOMLEN=4;HOMSEQ=CTCC;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 43395954 . A <DEL> 0 . END=43397152;SVTYPE=DEL;SVLEN=-1198;CIPOS=0,18;CIEND=0,18;HOMLEN=18;HOMSEQ=TGGTAAAACCCCATTTCT;NUM_MERGED_SVS=3;STDDEV_POS=0.00,0.00
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chr20 43643224 . A <DEL> 0 . END=43645948;SVTYPE=DEL;SVLEN=-2724;CIPOS=0,35;CIEND=0,35;HOMLEN=35;HOMSEQ=CCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGG;NUM_MERGED_SVS=3;STDDEV_POS=0.00,0.00
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chr20 43696486 . A <DUP:TANDEM> 0 . END=43696990;SVTYPE=DUP;SVLEN=504;CIPOS=0,23;CIEND=0,23;HOMLEN=23;HOMSEQ=CTGGGATTACAGGCGTGAGCCAC;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 44047485 . TTAACATCTGCACTAAGAAAAATTCCTCTGCCTTGGGATCCTGTTGATCTGTGACCTTACCCCCAACCCTGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCAATCCCTAATCTCAAGTAATCAGGGACACAAACACTGCGGAAGGCCGCAGGGTCCTCTGCCTAGGAAAACCAGAGACCTTTGTTCACTTGTTTATCTGCTGACCTTCCCTCCACTATTGTCCCATGACCCTGCCAAATCCCCCTCTGTGAGAAACACCCAAGAATTATCAATAAAAAAAAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA T 0 . END=44047884;SVTYPE=DEL;SVLEN=-399;CIGAR=1M399D;CIPOS=0,3;HOMLEN=3;HOMSEQ=TAA;NUM_MERGED_SVS=3;STDDEV_POS=0.00,0.00
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chr20 44134468 . ATAAATATATATTTATAATATATATTTATTATATATAAATAATATATATTTATAATAAATATATATAAATAAATATATATTTATAATATATATAAATAAATATATATTTATTATAAATATATATAAATATATATTTATTATAAATATAATAAATATATATTTATTATAAATATATAAATATTTATTATAAATATATATAAATATATATTTATAAATATTATAAATATATATACATTAATATATATTATAAATATATATT AAA 0 . END=44134726;SVTYPE=DEL;SVLEN=-258;CIGAR=1M2I258D;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 44404776 . T <INS> 0 . END=44404776;SVTYPE=INS;CIPOS=0,4;CIEND=0,4;HOMLEN=4;HOMSEQ=GTGT;LEFT_SVINSSEQ=GTGTTTGTTGATGTGTGTGTATGTGTGCGTGTGTGTGAATTGTGTGT;RIGHT_SVINSSEQ=TGTGTGTTGATGTGTGTGGAGTGTGTGGTGTGTGTGGTGTGTGGGTGTGTGGTGTGTGTGTGTGTTTGTGTGTGGTGTGTGTGCGTGTGTGTGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCAC;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 44677204 . G G]chr20:44683574] 0 . SVTYPE=BND;MATEID=MantaBND:2404:0:1:0:0:0:1;CIPOS=0,2;HOMLEN=2;HOMSEQ=CT;BND_DEPTH=19;MATE_BND_DEPTH=38;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 44680251 . C [chr20:44683272[C 0 . SVTYPE=BND;MATEID=MantaBND:2409:0:1:0:0:0:1;CIPOS=0,4;HOMLEN=4;HOMSEQ=AGGG;BND_DEPTH=19;MATE_BND_DEPTH=47;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 44683268 . C [chr20:44680255[C 0 . SVTYPE=BND;MATEID=MantaBND:2409:0:1:0:0:0:0;CIPOS=0,4;HOMLEN=4;HOMSEQ=CTGA;BND_DEPTH=47;MATE_BND_DEPTH=19;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 44683572 . C C]chr20:44677206] 0 . SVTYPE=BND;MATEID=MantaBND:2404:0:1:0:0:0:0;CIPOS=0,2;HOMLEN=2;HOMSEQ=AG;BND_DEPTH=38;MATE_BND_DEPTH=19;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 44764203 . C CATCCATCCATCCATCCATCCATCCGTCCATCCATTTATCCATCCATCCATCCATCCATCCATCCATCCATCCATTTATCCATCCGTCCATTTATCCATCCATCCATCCACCCACCCATCCATCCATCCATCCACTT 0 . END=44764203;SVTYPE=INS;SVLEN=136;CIGAR=1M136I;CIPOS=0,9;HOMLEN=9;HOMSEQ=ATCCATCCA;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 45575422 . A <DEL> 0 . END=45578660;SVTYPE=DEL;SVLEN=-3238;CIPOS=0,3;CIEND=0,3;HOMLEN=3;HOMSEQ=GCA;NUM_MERGED_SVS=2;STDDEV_POS=0.00,0.00
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chr20 45725015 . T TATACACACATATATATATATATATATATACACATATATATATATATACAC 0 . END=45725015;SVTYPE=INS;SVLEN=50;CIGAR=1M50I;CIPOS=0,3;HOMLEN=3;HOMSEQ=ATA;NUM_MERGED_SVS=3;STDDEV_POS=1.15,1.15
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chr20 45730773 . CTCACTGCAACCTCCGCTTCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCCGGGATTACAGGCACGTGCCACCACACCCAGCTAATTTTTCTATTTTTAGTA C 0 . END=45730885;SVTYPE=DEL;SVLEN=-112;CIGAR=1M112D;NUM_MERGED_SVS=2;STDDEV_POS=0.00,0.00
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chr20 45738910 . CTATATATAGTTATATATATAGTTATAGTTTACAAAACTATATATAGTTATATATAGTTATAGTTTACAAAACTATATATAGTTA C 0 . END=45738994;SVTYPE=DEL;SVLEN=-84;CIGAR=1M84D;CIPOS=0,14;HOMLEN=14;HOMSEQ=TATATATAGTTATA;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 45906708 . CGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGTTGGGCATGGTGGTGGGCGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGATCCTGGGAGGTGGAGGTTGCAGGGAGCCAGGATTGCACCACTGCACTCCAGCCTGGGTGACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAGATGGCATGAGGTTCCTTTCCCTTGGTTTCTCCTACCTCCTCCTTCGCTTCCCATGCCTGTGTGTTAGGTGTGATGGGAAAATACCTTTGCCCCACAGTAGACAGAGGTCATGGCTTAGAAAAAGGGAATTCATGGCCAGGCACAGTGGCTCATGCCTATAATCCCAGCACTTTGGGAGGCCAAGGTGGGCAGATCAGGAGGTCAGGAGATCGAGACCATCCCGGCCAACAT C 0 . END=45907144;SVTYPE=DEL;SVLEN=-436;CIGAR=1M436D;CIPOS=0,24;HOMLEN=24;HOMSEQ=GGTGAAACCCCGTCTCTACTAAAA;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 47156115 . CACACACACACACATATATATATATATATATATATATATATATATATATAT C 0 . END=47156165;SVTYPE=DEL;SVLEN=-50;CIGAR=1M50D;CIPOS=0,1;HOMLEN=1;HOMSEQ=A;NUM_MERGED_SVS=2;STDDEV_POS=0.00,0.00
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chr20 47390323 . CGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCCGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCGCCTCCTGT CTG 0 . END=47390651;SVTYPE=DEL;SVLEN=-328;CIGAR=1M2I328D;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 47481053 . T TTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 0 . END=47481053;SVTYPE=INS;SVLEN=50;CIGAR=1M50I;CIPOS=0,1;HOMLEN=1;HOMSEQ=T;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 47525638 . CGGGGCGGCTGGCCGGACGGGGGGGCTGACCCCCCCCACCTCCCTCCCGGACGGGGCGGCTGGCCGGGCGGGGGGCTGACCCCCCCACCTCCATCCCGGAGGGGGCGGCTGGCCGGGCGGGGGGCTGACCCCCCCCACCTCCCTCCCAGACGGGGCGGCTGGCCGGGCAGAGGGGCTCCTCACTTCCCAGTAGGGGCGGCCGGGCAGAGGTGCCCCTCACTTCCCGGATGGGG CAGGT 0 . END=47525870;SVTYPE=DEL;SVLEN=-232;CIGAR=1M4I232D;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 48010935 . C CATCACCATCATCACAACCACCATCGTCAATATCACCATCACTTTCATAATCACCACCACCACAACCACCATCAATATCACCATCACCTTAATCATCACCACAACCACCATCAAT 0 . END=48010935;SVTYPE=INS;SVLEN=114;CIGAR=1M114I;CIPOS=0,10;HOMLEN=10;HOMSEQ=ATCACCATCA;NUM_MERGED_SVS=3;STDDEV_POS=0.00,0.00
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chr20 48214211 . G G]chr20:48598465] 0 . SVTYPE=BND;MATEID=MantaBND:2577:0:1:0:0:0:0;IMPRECISE;CIPOS=-478,478;BND_DEPTH=22;MATE_BND_DEPTH=27;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 48214631 . C [chr20:48597827[C 0 . SVTYPE=BND;MATEID=MantaBND:2577:0:2:0:0:0:0;IMPRECISE;CIPOS=-472,473;BND_DEPTH=28;MATE_BND_DEPTH=31;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 48412705 . T TTCTTTCTTCTTAAGGTGTTACAGAAGGGCAAAGTCCATCTTCTGTTCCTTCCTTCCTTCTG 0 . END=48412705;SVTYPE=INS;SVLEN=61;CIGAR=1M61I;CIPOS=0,59;HOMLEN=59;HOMSEQ=TCTTTCTTCTTAAGGTGTTACAGAAGGGCAAAGTCCATCTTCTGTTCCTTCCTTCCTTC;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 48597827 . A [chr20:48214631[A 0 . SVTYPE=BND;MATEID=MantaBND:2577:0:2:0:0:0:1;IMPRECISE;CIPOS=-292,292;BND_DEPTH=31;MATE_BND_DEPTH=28;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 48598465 . C C]chr20:48214211] 0 . SVTYPE=BND;MATEID=MantaBND:2577:0:1:0:0:0:1;IMPRECISE;CIPOS=-311,311;BND_DEPTH=27;MATE_BND_DEPTH=22;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 48811623 . CCCCCC CACACGTGTGCATGCACACTACTGACCAGACCTGGATACACACACACACGTGCATGCACACTACTGACCAGACCTGGATACACACACACACACACGTGTGCATGCACACTACTGACCAGACCTGGATA 0 . END=48811628;SVTYPE=INS;SVLEN=127;CIGAR=1M127I5D;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 49108128 . CAAAAAAAAAAAAAGGCCAGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGACCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGCGGTGGCGGGCGCGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGCGCCACTGCAGTCCGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAA C 0 . END=49108453;SVTYPE=DEL;SVLEN=-325;CIGAR=1M325D;CIPOS=0,13;HOMLEN=13;HOMSEQ=AAAAAAAAAAAAA;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 49126606 . A <INS> 0 . END=49126641;SVTYPE=INS;LEFT_SVINSSEQ=AAAAAAAAAAAACTAAAAAATCAAACCAAAATAACCCAAAAAACTCAAAAAAAAAAAAAA;RIGHT_SVINSSEQ=GCTAAAGGGAGTTATGACCACCAAACTGCCCCCCAGCCTGGGAAAAAAAGAAAACCCCCTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAACAAAAAAACTTAAAAATCTAACCGATATTAGCCAAGACACTC;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 49834407 . ATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG A 0 . END=49834469;SVTYPE=DEL;SVLEN=-62;CIGAR=1M62D;CIPOS=0,10;HOMLEN=10;HOMSEQ=TATATATATA;NUM_MERGED_SVS=1;STDDEV_POS=0.00,0.00
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chr20 49927198 . CAAAGGTTGCAGTGAGCCGAGATGGTACCACTGCACTCCAGCCTGGGAACAAAGTGAGACTCCATCTCAAAAAAAAAAATA C 0 . END=49927278;SVTYPE=DEL;SVLEN=-80;CIGAR=1M80D;CIPOS=0,2;HOMLEN=2;HOMSEQ=AA;NUM_MERGED_SVS=3;STDDEV_POS=0.00,0.00

‎test_vcfs

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test/HG002_30x_Manta_v1.6.0_test_data.vcf.gz
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test/HG003_30x_Manta_v1.6.0_test_data.vcf.gz
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test/HG004_30x_Manta_v1.6.0_test_data.vcf.gz

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