text: user1770: Many popular SV callers output a VCF. Unfortunately, there isn't a unified system at the present to label events with the same notation. 
  However, is there a standard method for converting these VCFs to BEDPEs? 
  svtools comes to mind: https://github.com/hall-lab/svtools
  There are also some Bioconductor packages. 
  However, is there currently a standard widely used? Normally this is because a certain consortium did it in a certain way. 
  EDIT: There was a question in the comments about VCF vs BEDPE for structural variants.
  https://github.com/jaquol/blog-like-old/blob/master/01-How-interpret-structural-variants-BEDPE-format.md
  This is a structural variant in VCF format:
  ##fileformat=VCFv4.2                                    
  ##source=LUMPY                                  
  ##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=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">                                   
  ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">                                    
  ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">                                    
  ##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">                                  
  #CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  3128_T47D
  chr1    1584528 11  N   <DUP>   .   .   SVTYPE=DUP;STRANDS=-+:6;SVLEN=66541;END=1651069;CIPOS=-449,10;CIEND=-10,503;CIPOS95=-374,0;CIEND95=0,366;IMPRECISE;SU=6;PE=6;SR=0;PRPOS=2.44491e-07,3.26458e-07,4.33697e-07,5.7608e-07,7.57136e-07,9.87322e-07,1.28796e-06,1.66553e-06,2.14862e-06,2.75607e-06,3.52645e-06,4.48654e-06,5.68684e-06,7.14253e-06,8.95608e-06,1.11311e-05,1.38146e-05,1.70081e-05,2.09074e-05,2.54614e-05,3.0947e-05,3.7325e-05,4.47552e-05,5.33515e-05,6.32491e-05,7.45332e-05,8.7438e-05,0.00010173,0.000117821,0.000135629,0.000155258,0.000177125,0.000200949,0.000227194,0.000255827,0.000286183,0.000319177,0.000353501,0.000390203,0.000428746,0.000468895,0.000511378,0.000555476,0.000600756,0.000648001,0.000695831,0.000745204,0.000795631,0.000845517,0.000896997,0.00094752,0.000998877,0.00104988,0.00110053,0.00115056,0.00120038,0.00124937,0.00129849,0.00134617,0.00139206,0.00143762,0.0014814,0.00152386,0.00156521,0.00160519,0.00164404,0.00168131,0.00171717,0.00175139,0.00178475,0.00181657,0.00184663,0.00187563,0.00190327,0.00192975,0.00195479,0.00197842,0.00200183,0.00202369,0.00204549,0.00206583,0.00208582,0.00210445,0.00212224,0.00213857,0.00215452,0.00216896,0.00218263,0.00219584,0.00220845,0.00221975,0.00223061,0.00224049,0.00224956,0.00225841,0.00226617,0.00227317,0.00227931,0.00228505,0.00228996,0.00229495,0.00229948,0.00230347,0.00230755,0.00231109,0.0023146,0.00231767,0.00232087,0.0023235,0.00232593,0.00232843,0.00233037,0.00233266,0.00233471,0.0023365,0.00233822,0.00233974,0.00234121,0.00234261,0.00234391,0.00234524,0.00234656,0.00234787,0.00234901,0.00235006,0.0023513,0.0023522,0.00235324,0.00235429,0.00235519,0.00235614,0.00235695,0.00235786,0.00235864,0.00235957,0.00236033,0.00236117,0.00236198,0.00236288,0.00236365,0.00236441,0.00236514,0.00236581,0.00236671,0.0023675,0.00236851,0.0023693,0.00237023,0.00237106,0.00237196,0.00237283,0.00237371,0.00237471,0.00237556,0.00237647,0.00237733,0.00237819,0.00237897,0.00237973,0.00238056,0.00238145,0.00238222,0.00238294,0.00238394,0.0023848,0.00238545,0.00238618,0.0023871,0.00238796,0.0023889,0.00238976,0.00239053,0.00239142,0.00239222,0.0023932,0.00239412,0.00239504,0.00239599,0.00239704,0.00239815,0.00239902,0.00239984,0.00240073,0.00240184,0.00240288,0.00240385,0.00240489,0.00240597,0.00240695,0.00240787,0.00240872,0.00240953,0.00241046,0.00241129,0.00241228,0.00241313,0.00241411,0.00241502,0.00241603,0.00241712,0.00241811,0.00241934,0.00242034,0.00242141,0.00242256,0.00242369,0.00242488,0.00242598,0.00242723,0.00242845,0.00242958,0.00243082,0.00243182,0.00243282,0.00243389,0.00243485,0.00243593,0.00243699,0.00243818,0.00243921,0.00244038,0.00244162,0.00244278,0.00244386,0.002445,0.00244621,0.00244734,0.00244858,0.00244991,0.0024512,0.00245246,0.00245379,0.00245524,0.00245665,0.00245774,0.00245913,0.00246048,0.00246179,0.00246295,0.00246419,0.00246564,0.00246697,0.00246825,0.00246954,0.0024709,0.00247228,0.00247353,0.002475,0.00247639,0.00247812,0.0024795,0.00248075,0.00248215,0.00248359,0.00248517,0.00248655,0.00248793,0.00248927,0.00249072,0.00249223,0.00249351,0.00249512,0.00249648,0.00249801,0.00249976,0.00250133,0.00250293,0.00250464,0.00250618,0.00250758,0.00250932,0.00251113,0.00251256,0.00251406,0.00251567,0.00251749,0.00251919,0.00252051,0.00252197,0.00252351,0.00252518,0.00252675,0.00252834,0.00252988,0.00253136,0.00253307,0.00253469,0.00253652,0.0025383,0.0025403,0.00254212,0.00254387,0.00254575,0.00254754,0.00254942,0.0025514,0.00255316,0.00255534,0.0025573,0.00255935,0.00256123,0.00256313,0.00256486,0.00256668,0.00256838,0.00257033,0.00257235,0.00257408,0.00257612,0.00257812,0.00258004,0.00258208,0.00258394,0.00258613,0.00258805,0.00259035,0.00259238,0.00259449,0.00259664,0.00259868,0.00260091,0.0026033,0.00260538,0.00260742,0.00260951,0.00261187,0.00261382,0.00261579,0.00261808,0.00262029,0.00262253,0.00262481,0.00262695,0.00262929,0.00263173,0.00263396,0.0026362,0.00263851,0.00264069,0.00264344,0.0026458,0.00264821,0.00265024,0.00265247,0.00265488,0.00265735,0.00265965,0.00266185,0.00266402,0.00266663,0.00266919,0.00267144,0.00267383,0.00267621,0.002679,0.00268127,0.00268393,0.00268632,0.00268891,0.00269145,0.00269389,0.00269661,0.00269912,0.00270165,0.00270404,0.0027067,0.00270939,0.00271195,0.00271455,0.00271722,0.00271969,0.00272252,0.0027254,0.002728,0.00273082,0.00273369,0.00273648,0.00273952,0.00274227,0.00274511,0.00274816,0.00275103,0.00275394,0.00275687,0.00275977,0.00276241,0.00276495,0.00276767,0.00277064,0.00277351,0.00277641,0.00277909,0.00278202,0.00278452,0.00278729,0.00278998,0.00279275,0.0027958,0.00279878,0.0028016,0.00280472,0.00280771,0.0028109,0.00281415,0.00281717,0.00282038,0.00282346,0.00282626,0.00282919,0.00283207,0.00283518,0.00283843,0.00284122,0.0028439,0.00284708,0.00284994,0.00285294,0.00285587,0.00285848,0.00286126,0.0028643,0.00286701,0.00287003,0.00287284,0.00287589,0.00287886,0.00288176,0.00288469,0.00288762,0.0028909,0.00289392,0.00289664,0.00289945,0.00290244,0.00290543,0.00290824,0.00291089,0.00291354,0.00291634,0.00291902,0.00292172,0.00292413,0.0029271,0.00292984,0.002933,0.0029355,0.00293802,0.0029405,0.00294333,0.00294613,0.00117372,0.000467584,0.000186264,7.42093e-05,2.95642e-05,1.17781e-05,4.69226e-06,1.86919e-06,7.44696e-07,2.96676e-07;PREND=3.02026e-15,4.78471e-14,7.57973e-13,1.20067e-11,1.90178e-10,3.01282e-09,4.77324e-08,7.56151e-07,1.19779e-05,0.000189743,0.00300582,0.0030039,0.00300127,0.00299837,0.00299541,0.00299255,0.00299047,0.00298793,0.00298555,0.00298267,0.00298033,0.0029782,0.00297579,0.00297295,0.00297017,0.00296769,0.00296562,0.0029632,0.00296072,0.00295816,0.00295557,0.00295308,0.00295062,0.0029479,0.0029447,0.00294211,0.00293963,0.00293734,0.00293449,0.00293173,0.00292904,0.0029266,0.00292425,0.00292122,0.00291848,0.00291567,0.00291333,0.00291077,0.00290832,0.00290537,0.00290246,0.00289957,0.00289704,0.00289385,0.00289114,0.0028884,0.00288549,0.00288284,0.00287995,0.00287726,0.00287463,0.00287144,0.00286885,0.00286569,0.0028629,0.00286073,0.00285801,0.00285472,0.00285196,0.00284879,0.00284594,0.00284346,0.00284056,0.00283777,0.00283502,0.0028323,0.00282939,0.00282645,0.00282353,0.00282053,0.00281778,0.00281457,0.00281189,0.00280891,0.00280615,0.00280355,0.00280057,0.00279736,0.00279468,0.00279185,0.00278916,0.00278699,0.0027844,0.00278164,0.00277904,0.00277575,0.00277311,0.00277044,0.00276776,0.00276461,0.00276186,0.00275906,0.00275677,0.00275435,0.00275168,0.00274942,0.00274617,0.00274363,0.00274107,0.00273819,0.0027355,0.00273297,0.00273059,0.00272816,0.00272563,0.00272344,0.00272085,0.00271833,0.00271609,0.00271369,0.00271133,0.00270894,0.0027064,0.00270412,0.00270171,0.0026994,0.00269703,0.00269418,0.00269178,0.00268936,0.00268728,0.00268506,0.00268312,0.00268036,0.00267787,0.00267564,0.00267347,0.00267118,0.00266877,0.00266653,0.00266441,0.00266271,0.00266054,0.00265825,0.0026559,0.00265383,0.00265161,0.00264968,0.00264732,0.00264539,0.00264295,0.00264098,0.00263869,0.00263636,0.00263434,0.00263215,0.00263023,0.00262822,0.00262628,0.00262422,0.00262236,0.00262036,0.00261831,0.00261628,0.00261451,0.00261257,0.00261059,0.00260871,0.00260687,0.00260501,0.00260267,0.00260094,0.00259868,0.00259649,0.00259478,0.00259308,0.00259143,0.00258955,0.00258721,0.00258551,0.00258347,0.00258174,0.00258005,0.00257832,0.00257656,0.00257497,0.00257335,0.00257165,0.00256984,0.00256803,0.00256624,0.00256436,0.00256254,0.0025607,0.00255925,0.00255792,0.00255616,0.00255439,0.0025528,0.00255149,0.00254971,0.00254832,0.00254703,0.00254555,0.00254428,0.00254283,0.00254166,0.00254023,0.00253862,0.00253728,0.002536,0.00253436,0.00253252,0.00253096,0.00252943,0.00252819,0.00252656,0.00252508,0.00252379,0.00252243,0.00252084,0.00251975,0.00251831,0.00251666,0.00251521,0.00251391,0.00251267,0.00251144,0.00251024,0.00250897,0.00250758,0.00250646,0.00250525,0.00250396,0.00250248,0.00250084,0.00249962,0.00249836,0.00249712,0.00249567,0.00249435,0.00249341,0.00249217,0.00249093,0.00248988,0.00248849,0.00248716,0.00248589,0.00248488,0.00248398,0.00248264,0.00248155,0.00248047,0.00247944,0.00247824,0.00247724,0.00247609,0.00247492,0.00247375,0.00247262,0.00247147,0.0024706,0.00246888,0.0024678,0.00246675,0.00246572,0.00246487,0.00246414,0.00246316,0.0024619,0.00246083,0.00245995,0.00245894,0.002458,0.0024569,0.00245599,0.00245492,0.0024538,0.00245275,0.0024515,0.00245035,0.0024494,0.00244835,0.00244731,0.00244625,0.00244542,0.00244473,0.0024439,0.00244295,0.00244172,0.00244076,0.00243982,0.00243907,0.00243812,0.00243725,0.00243639,0.00243555,0.00243464,0.0024338,0.00243277,0.00243145,0.00243048,0.00242965,0.0024285,0.00242736,0.00242654,0.00242575,0.00242483,0.00242391,0.00242298,0.00242193,0.00242078,0.00241981,0.00241862,0.00241771,0.00241663,0.0024155,0.0024146,0.00241367,0.0024125,0.00241116,0.00241008,0.00240902,0.00240729,0.00240548,0.00240419,0.00240253,0.00240081,0.00239908,0.00239741,0.00239517,0.0023929,0.00239052,0.00238798,0.00238505,0.00238189,0.00237904,0.00237565,0.00237201,0.00236829,0.00236374,0.00235923,0.00235403,0.00234858,0.00234288,0.00233677,0.00233038,0.00232438,0.0023171,0.00230981,0.00230198,0.00229329,0.00228476,0.00227551,0.00226594,0.00225598,0.00224564,0.00223392,0.00222138,0.00220881,0.00219607,0.00218362,0.00217038,0.00215639,0.00214182,0.00212751,0.00211102,0.00209334,0.00207535,0.00205704,0.00203711,0.00201595,0.00199504,0.00197257,0.00194934,0.0019241,0.00189856,0.0018717,0.00184359,0.00181463,0.00178446,0.00175283,0.0017206,0.0016859,0.00165096,0.00161563,0.00157919,0.00154094,0.00150137,0.00146059,0.00141945,0.00137825,0.0013367,0.00129363,0.00124908,0.00120422,0.00115974,0.00111459,0.00106967,0.00102485,0.000979928,0.000935386,0.000891343,0.000847616,0.000805325,0.000763099,0.000721605,0.000680876,0.000641258,0.000602415,0.000564516,0.000529212,0.000494813,0.000461726,0.000429703,0.000398541,0.000369522,0.000342268,0.000316742,0.000292816,0.000270237,0.000249087,0.000228998,0.000210083,0.000192775,0.000176194,0.000160682,0.000146541,0.000133475,0.000121171,0.000110027,9.98983e-05,9.04025e-05,8.1898e-05,7.37485e-05,6.64247e-05,5.991e-05,5.34662e-05,4.79254e-05,4.28124e-05,3.80863e-05,3.37871e-05,2.98488e-05,2.64158e-05,2.31778e-05,2.02341e-05,1.77006e-05,1.53314e-05,1.32501e-05,1.13287e-05,9.72139e-06,8.17381e-06,6.84904e-06,5.73097e-06,4.74769e-06,3.91083e-06,3.20076e-06,2.6024e-06,2.08961e-06,1.69223e-06,1.36759e-06,1.08247e-06,8.47588e-07,6.69622e-07,5.17384e-07,4.00954e-07,3.11072e-07,2.34849e-07,1.76165e-07,1.31673e-07,9.73364e-08,7.19841e-08,5.32892e-08,3.90585e-08,2.83402e-08,2.02418e-08,1.4579e-08,1.06446e-08,7.59531e-09,5.37474e-09,3.79538e-09,2.64724e-09,1.84573e-09,1.29566e-09,9.10203e-10,6.14793e-10,4.26199e-10,2.87287e-10,1.936e-10,1.30732e-10,9.00388e-11,6.2542e-11,4.32799e-11,2.90205e-11,1.95416e-11,1.3365e-11,8.69465e-12,5.75237e-12,3.71099e-12,2.54394e-12,1.73591e-12,1.14175e-12,7.46542e-13,4.68409e-13,3.08728e-13,1.94589e-13,1.17053e-13,7.58227e-14,4.59278e-14,2.89681e-14,1.97988e-14,1.19182e-14,7.29947e-15,4.37438e-15  GT:SU:PE:SR ./.:6:6:0
  
  And here is the same event as a BEDPE:
  chr1    1584078 1584538 chr1    1651058 1651572 11  .   -   +   DUP .   SVTYPE=DUP;SVLEN=66541;END=1651069;STRANDS=-+:6;IMPRECISE;CIPOS=-449,10;CIEND=-10...
  
  https://github.com/cancerit/BRASS/wiki/BEDPE
  The following is a table describing how SVs are represented in BEDPE format:
  Heading Type    Description
  chr1    String  Chromosome of lower coordinate
  start1  0-based int Start coordinate of lower coordinate
  end1    1-based int End coordinate of lower coordinate
  chr2    String  Chromosome of high coordinate
  start2  0-based int Start coordinate of high coordinate
  end2    1-based int End coordinate of high coordinate
  id/name String  ID of event, correlates with VCF
  brass_score int Number of aberrant pairs contributing to the rearrangement group.
  strand1 [+-]    Strand of end in 'genomic' context - see table
  strand2 [+-]    Strand of end in 'genomic' context
  
  
  user681: SURVIVOR has a subcommand to convert an SV vcf to bed, although I'm not sure if it's actual bedpe format.
  To install:
  git clone https://github.com/fritzsedlazeck/SURVIVOR.git
  cd SURVIVOR/Debug
  make
  
  Then:
  ./SURVIVOR vcftobed input.vcf $minSize $maxSize output.bed
  
  If you run this on your example file, you get:
  $ ./SURVIVOR vcftobed foo.vcf 1 10000000000000000 bar.bed; cat bar.bed 
  chr1    1584528 1584528 chr1    1651069 1651069 11  ,   -   +   DUP
  
  
original_text: 1770: <p>Many popular SV callers output a VCF. Unfortunately, there isn't a unified system at the present to label events with the same notation. </p>
  
  <p>However, is there a standard method for converting these VCFs to BEDPEs? </p>
  
  <p>svtools comes to mind: <a href="https://github.com/hall-lab/svtools" rel="nofollow noreferrer">https://github.com/hall-lab/svtools</a></p>
  
  <p>There are also some Bioconductor packages. </p>
  
  <p>However, is there currently a standard widely used? Normally this is because a certain consortium did it in a certain way. </p>
  
  <p>EDIT: There was a question in the comments about VCF vs BEDPE for structural variants.</p>
  
  <p><a href="https://github.com/jaquol/blog-like-old/blob/master/01-How-interpret-structural-variants-BEDPE-format.md" rel="nofollow noreferrer">https://github.com/jaquol/blog-like-old/blob/master/01-How-interpret-structural-variants-BEDPE-format.md</a></p>
  
  <p>This is a structural variant in VCF format:</p>
  
  <pre><code>##fileformat=VCFv4.2                                    
  ##source=LUMPY                                  
  ##INFO=&lt;ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"&gt;                                    
  ##INFO=&lt;ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"&gt;                                  
  ##INFO=&lt;ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"&gt;                                    
  ##INFO=&lt;ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"&gt;                                  
  ##INFO=&lt;ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"&gt;                                   
  ##INFO=&lt;ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"&gt;                                 
  ##INFO=&lt;ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"&gt;                                 
  ##INFO=&lt;ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"&gt;                                 
  ##INFO=&lt;ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"&gt;                                 
  ##INFO=&lt;ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"&gt;                                  
  ##INFO=&lt;ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"&gt;                                 
  ##INFO=&lt;ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"&gt;                                  
  ##INFO=&lt;ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"&gt;                                   
  ##INFO=&lt;ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"&gt;                                 
  ##INFO=&lt;ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"&gt;                                  
  ##INFO=&lt;ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"&gt;                                   
  ##INFO=&lt;ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"&gt;                                    
  ##INFO=&lt;ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"&gt;                                    
  ##ALT=&lt;ID=DEL,Description="Deletion"&gt;                                   
  ##ALT=&lt;ID=DUP,Description="Duplication"&gt;                                    
  ##ALT=&lt;ID=INV,Description="Inversion"&gt;                                  
  ##ALT=&lt;ID=DUP:TANDEM,Description="Tandem duplication"&gt;                                  
  ##ALT=&lt;ID=INS,Description="Insertion of novel sequence"&gt;                                    
  ##ALT=&lt;ID=CNV,Description="Copy number variable region"&gt;                                    
  ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description="Genotype"&gt;                                    
  ##FORMAT=&lt;ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"&gt;                                    
  ##FORMAT=&lt;ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"&gt;                                  
  ##FORMAT=&lt;ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"&gt;                                   
  ##FORMAT=&lt;ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"&gt;                                  
  #CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  3128_T47D
  chr1    1584528 11  N   &lt;DUP&gt;   .   .   SVTYPE=DUP;STRANDS=-+:6;SVLEN=66541;END=1651069;CIPOS=-449,10;CIEND=-10,503;CIPOS95=-374,0;CIEND95=0,366;IMPRECISE;SU=6;PE=6;SR=0;PRPOS=2.44491e-07,3.26458e-07,4.33697e-07,5.7608e-07,7.57136e-07,9.87322e-07,1.28796e-06,1.66553e-06,2.14862e-06,2.75607e-06,3.52645e-06,4.48654e-06,5.68684e-06,7.14253e-06,8.95608e-06,1.11311e-05,1.38146e-05,1.70081e-05,2.09074e-05,2.54614e-05,3.0947e-05,3.7325e-05,4.47552e-05,5.33515e-05,6.32491e-05,7.45332e-05,8.7438e-05,0.00010173,0.000117821,0.000135629,0.000155258,0.000177125,0.000200949,0.000227194,0.000255827,0.000286183,0.000319177,0.000353501,0.000390203,0.000428746,0.000468895,0.000511378,0.000555476,0.000600756,0.000648001,0.000695831,0.000745204,0.000795631,0.000845517,0.000896997,0.00094752,0.000998877,0.00104988,0.00110053,0.00115056,0.00120038,0.00124937,0.00129849,0.00134617,0.00139206,0.00143762,0.0014814,0.00152386,0.00156521,0.00160519,0.00164404,0.00168131,0.00171717,0.00175139,0.00178475,0.00181657,0.00184663,0.00187563,0.00190327,0.00192975,0.00195479,0.00197842,0.00200183,0.00202369,0.00204549,0.00206583,0.00208582,0.00210445,0.00212224,0.00213857,0.00215452,0.00216896,0.00218263,0.00219584,0.00220845,0.00221975,0.00223061,0.00224049,0.00224956,0.00225841,0.00226617,0.00227317,0.00227931,0.00228505,0.00228996,0.00229495,0.00229948,0.00230347,0.00230755,0.00231109,0.0023146,0.00231767,0.00232087,0.0023235,0.00232593,0.00232843,0.00233037,0.00233266,0.00233471,0.0023365,0.00233822,0.00233974,0.00234121,0.00234261,0.00234391,0.00234524,0.00234656,0.00234787,0.00234901,0.00235006,0.0023513,0.0023522,0.00235324,0.00235429,0.00235519,0.00235614,0.00235695,0.00235786,0.00235864,0.00235957,0.00236033,0.00236117,0.00236198,0.00236288,0.00236365,0.00236441,0.00236514,0.00236581,0.00236671,0.0023675,0.00236851,0.0023693,0.00237023,0.00237106,0.00237196,0.00237283,0.00237371,0.00237471,0.00237556,0.00237647,0.00237733,0.00237819,0.00237897,0.00237973,0.00238056,0.00238145,0.00238222,0.00238294,0.00238394,0.0023848,0.00238545,0.00238618,0.0023871,0.00238796,0.0023889,0.00238976,0.00239053,0.00239142,0.00239222,0.0023932,0.00239412,0.00239504,0.00239599,0.00239704,0.00239815,0.00239902,0.00239984,0.00240073,0.00240184,0.00240288,0.00240385,0.00240489,0.00240597,0.00240695,0.00240787,0.00240872,0.00240953,0.00241046,0.00241129,0.00241228,0.00241313,0.00241411,0.00241502,0.00241603,0.00241712,0.00241811,0.00241934,0.00242034,0.00242141,0.00242256,0.00242369,0.00242488,0.00242598,0.00242723,0.00242845,0.00242958,0.00243082,0.00243182,0.00243282,0.00243389,0.00243485,0.00243593,0.00243699,0.00243818,0.00243921,0.00244038,0.00244162,0.00244278,0.00244386,0.002445,0.00244621,0.00244734,0.00244858,0.00244991,0.0024512,0.00245246,0.00245379,0.00245524,0.00245665,0.00245774,0.00245913,0.00246048,0.00246179,0.00246295,0.00246419,0.00246564,0.00246697,0.00246825,0.00246954,0.0024709,0.00247228,0.00247353,0.002475,0.00247639,0.00247812,0.0024795,0.00248075,0.00248215,0.00248359,0.00248517,0.00248655,0.00248793,0.00248927,0.00249072,0.00249223,0.00249351,0.00249512,0.00249648,0.00249801,0.00249976,0.00250133,0.00250293,0.00250464,0.00250618,0.00250758,0.00250932,0.00251113,0.00251256,0.00251406,0.00251567,0.00251749,0.00251919,0.00252051,0.00252197,0.00252351,0.00252518,0.00252675,0.00252834,0.00252988,0.00253136,0.00253307,0.00253469,0.00253652,0.0025383,0.0025403,0.00254212,0.00254387,0.00254575,0.00254754,0.00254942,0.0025514,0.00255316,0.00255534,0.0025573,0.00255935,0.00256123,0.00256313,0.00256486,0.00256668,0.00256838,0.00257033,0.00257235,0.00257408,0.00257612,0.00257812,0.00258004,0.00258208,0.00258394,0.00258613,0.00258805,0.00259035,0.00259238,0.00259449,0.00259664,0.00259868,0.00260091,0.0026033,0.00260538,0.00260742,0.00260951,0.00261187,0.00261382,0.00261579,0.00261808,0.00262029,0.00262253,0.00262481,0.00262695,0.00262929,0.00263173,0.00263396,0.0026362,0.00263851,0.00264069,0.00264344,0.0026458,0.00264821,0.00265024,0.00265247,0.00265488,0.00265735,0.00265965,0.00266185,0.00266402,0.00266663,0.00266919,0.00267144,0.00267383,0.00267621,0.002679,0.00268127,0.00268393,0.00268632,0.00268891,0.00269145,0.00269389,0.00269661,0.00269912,0.00270165,0.00270404,0.0027067,0.00270939,0.00271195,0.00271455,0.00271722,0.00271969,0.00272252,0.0027254,0.002728,0.00273082,0.00273369,0.00273648,0.00273952,0.00274227,0.00274511,0.00274816,0.00275103,0.00275394,0.00275687,0.00275977,0.00276241,0.00276495,0.00276767,0.00277064,0.00277351,0.00277641,0.00277909,0.00278202,0.00278452,0.00278729,0.00278998,0.00279275,0.0027958,0.00279878,0.0028016,0.00280472,0.00280771,0.0028109,0.00281415,0.00281717,0.00282038,0.00282346,0.00282626,0.00282919,0.00283207,0.00283518,0.00283843,0.00284122,0.0028439,0.00284708,0.00284994,0.00285294,0.00285587,0.00285848,0.00286126,0.0028643,0.00286701,0.00287003,0.00287284,0.00287589,0.00287886,0.00288176,0.00288469,0.00288762,0.0028909,0.00289392,0.00289664,0.00289945,0.00290244,0.00290543,0.00290824,0.00291089,0.00291354,0.00291634,0.00291902,0.00292172,0.00292413,0.0029271,0.00292984,0.002933,0.0029355,0.00293802,0.0029405,0.00294333,0.00294613,0.00117372,0.000467584,0.000186264,7.42093e-05,2.95642e-05,1.17781e-05,4.69226e-06,1.86919e-06,7.44696e-07,2.96676e-07;PREND=3.02026e-15,4.78471e-14,7.57973e-13,1.20067e-11,1.90178e-10,3.01282e-09,4.77324e-08,7.56151e-07,1.19779e-05,0.000189743,0.00300582,0.0030039,0.00300127,0.00299837,0.00299541,0.00299255,0.00299047,0.00298793,0.00298555,0.00298267,0.00298033,0.0029782,0.00297579,0.00297295,0.00297017,0.00296769,0.00296562,0.0029632,0.00296072,0.00295816,0.00295557,0.00295308,0.00295062,0.0029479,0.0029447,0.00294211,0.00293963,0.00293734,0.00293449,0.00293173,0.00292904,0.0029266,0.00292425,0.00292122,0.00291848,0.00291567,0.00291333,0.00291077,0.00290832,0.00290537,0.00290246,0.00289957,0.00289704,0.00289385,0.00289114,0.0028884,0.00288549,0.00288284,0.00287995,0.00287726,0.00287463,0.00287144,0.00286885,0.00286569,0.0028629,0.00286073,0.00285801,0.00285472,0.00285196,0.00284879,0.00284594,0.00284346,0.00284056,0.00283777,0.00283502,0.0028323,0.00282939,0.00282645,0.00282353,0.00282053,0.00281778,0.00281457,0.00281189,0.00280891,0.00280615,0.00280355,0.00280057,0.00279736,0.00279468,0.00279185,0.00278916,0.00278699,0.0027844,0.00278164,0.00277904,0.00277575,0.00277311,0.00277044,0.00276776,0.00276461,0.00276186,0.00275906,0.00275677,0.00275435,0.00275168,0.00274942,0.00274617,0.00274363,0.00274107,0.00273819,0.0027355,0.00273297,0.00273059,0.00272816,0.00272563,0.00272344,0.00272085,0.00271833,0.00271609,0.00271369,0.00271133,0.00270894,0.0027064,0.00270412,0.00270171,0.0026994,0.00269703,0.00269418,0.00269178,0.00268936,0.00268728,0.00268506,0.00268312,0.00268036,0.00267787,0.00267564,0.00267347,0.00267118,0.00266877,0.00266653,0.00266441,0.00266271,0.00266054,0.00265825,0.0026559,0.00265383,0.00265161,0.00264968,0.00264732,0.00264539,0.00264295,0.00264098,0.00263869,0.00263636,0.00263434,0.00263215,0.00263023,0.00262822,0.00262628,0.00262422,0.00262236,0.00262036,0.00261831,0.00261628,0.00261451,0.00261257,0.00261059,0.00260871,0.00260687,0.00260501,0.00260267,0.00260094,0.00259868,0.00259649,0.00259478,0.00259308,0.00259143,0.00258955,0.00258721,0.00258551,0.00258347,0.00258174,0.00258005,0.00257832,0.00257656,0.00257497,0.00257335,0.00257165,0.00256984,0.00256803,0.00256624,0.00256436,0.00256254,0.0025607,0.00255925,0.00255792,0.00255616,0.00255439,0.0025528,0.00255149,0.00254971,0.00254832,0.00254703,0.00254555,0.00254428,0.00254283,0.00254166,0.00254023,0.00253862,0.00253728,0.002536,0.00253436,0.00253252,0.00253096,0.00252943,0.00252819,0.00252656,0.00252508,0.00252379,0.00252243,0.00252084,0.00251975,0.00251831,0.00251666,0.00251521,0.00251391,0.00251267,0.00251144,0.00251024,0.00250897,0.00250758,0.00250646,0.00250525,0.00250396,0.00250248,0.00250084,0.00249962,0.00249836,0.00249712,0.00249567,0.00249435,0.00249341,0.00249217,0.00249093,0.00248988,0.00248849,0.00248716,0.00248589,0.00248488,0.00248398,0.00248264,0.00248155,0.00248047,0.00247944,0.00247824,0.00247724,0.00247609,0.00247492,0.00247375,0.00247262,0.00247147,0.0024706,0.00246888,0.0024678,0.00246675,0.00246572,0.00246487,0.00246414,0.00246316,0.0024619,0.00246083,0.00245995,0.00245894,0.002458,0.0024569,0.00245599,0.00245492,0.0024538,0.00245275,0.0024515,0.00245035,0.0024494,0.00244835,0.00244731,0.00244625,0.00244542,0.00244473,0.0024439,0.00244295,0.00244172,0.00244076,0.00243982,0.00243907,0.00243812,0.00243725,0.00243639,0.00243555,0.00243464,0.0024338,0.00243277,0.00243145,0.00243048,0.00242965,0.0024285,0.00242736,0.00242654,0.00242575,0.00242483,0.00242391,0.00242298,0.00242193,0.00242078,0.00241981,0.00241862,0.00241771,0.00241663,0.0024155,0.0024146,0.00241367,0.0024125,0.00241116,0.00241008,0.00240902,0.00240729,0.00240548,0.00240419,0.00240253,0.00240081,0.00239908,0.00239741,0.00239517,0.0023929,0.00239052,0.00238798,0.00238505,0.00238189,0.00237904,0.00237565,0.00237201,0.00236829,0.00236374,0.00235923,0.00235403,0.00234858,0.00234288,0.00233677,0.00233038,0.00232438,0.0023171,0.00230981,0.00230198,0.00229329,0.00228476,0.00227551,0.00226594,0.00225598,0.00224564,0.00223392,0.00222138,0.00220881,0.00219607,0.00218362,0.00217038,0.00215639,0.00214182,0.00212751,0.00211102,0.00209334,0.00207535,0.00205704,0.00203711,0.00201595,0.00199504,0.00197257,0.00194934,0.0019241,0.00189856,0.0018717,0.00184359,0.00181463,0.00178446,0.00175283,0.0017206,0.0016859,0.00165096,0.00161563,0.00157919,0.00154094,0.00150137,0.00146059,0.00141945,0.00137825,0.0013367,0.00129363,0.00124908,0.00120422,0.00115974,0.00111459,0.00106967,0.00102485,0.000979928,0.000935386,0.000891343,0.000847616,0.000805325,0.000763099,0.000721605,0.000680876,0.000641258,0.000602415,0.000564516,0.000529212,0.000494813,0.000461726,0.000429703,0.000398541,0.000369522,0.000342268,0.000316742,0.000292816,0.000270237,0.000249087,0.000228998,0.000210083,0.000192775,0.000176194,0.000160682,0.000146541,0.000133475,0.000121171,0.000110027,9.98983e-05,9.04025e-05,8.1898e-05,7.37485e-05,6.64247e-05,5.991e-05,5.34662e-05,4.79254e-05,4.28124e-05,3.80863e-05,3.37871e-05,2.98488e-05,2.64158e-05,2.31778e-05,2.02341e-05,1.77006e-05,1.53314e-05,1.32501e-05,1.13287e-05,9.72139e-06,8.17381e-06,6.84904e-06,5.73097e-06,4.74769e-06,3.91083e-06,3.20076e-06,2.6024e-06,2.08961e-06,1.69223e-06,1.36759e-06,1.08247e-06,8.47588e-07,6.69622e-07,5.17384e-07,4.00954e-07,3.11072e-07,2.34849e-07,1.76165e-07,1.31673e-07,9.73364e-08,7.19841e-08,5.32892e-08,3.90585e-08,2.83402e-08,2.02418e-08,1.4579e-08,1.06446e-08,7.59531e-09,5.37474e-09,3.79538e-09,2.64724e-09,1.84573e-09,1.29566e-09,9.10203e-10,6.14793e-10,4.26199e-10,2.87287e-10,1.936e-10,1.30732e-10,9.00388e-11,6.2542e-11,4.32799e-11,2.90205e-11,1.95416e-11,1.3365e-11,8.69465e-12,5.75237e-12,3.71099e-12,2.54394e-12,1.73591e-12,1.14175e-12,7.46542e-13,4.68409e-13,3.08728e-13,1.94589e-13,1.17053e-13,7.58227e-14,4.59278e-14,2.89681e-14,1.97988e-14,1.19182e-14,7.29947e-15,4.37438e-15  GT:SU:PE:SR ./.:6:6:0
  </code></pre>
  
  <p>And here is the same event as a BEDPE:</p>
  
  <pre><code>chr1    1584078 1584538 chr1    1651058 1651572 11  .   -   +   DUP .   SVTYPE=DUP;SVLEN=66541;END=1651069;STRANDS=-+:6;IMPRECISE;CIPOS=-449,10;CIEND=-10...
  </code></pre>
  
  <p><a href="https://github.com/cancerit/BRASS/wiki/BEDPE" rel="nofollow noreferrer">https://github.com/cancerit/BRASS/wiki/BEDPE</a></p>
  
  <p>The following is a table describing how SVs are represented in BEDPE format:</p>
  
  <pre><code>Heading Type    Description
  chr1    String  Chromosome of lower coordinate
  start1  0-based int Start coordinate of lower coordinate
  end1    1-based int End coordinate of lower coordinate
  chr2    String  Chromosome of high coordinate
  start2  0-based int Start coordinate of high coordinate
  end2    1-based int End coordinate of high coordinate
  id/name String  ID of event, correlates with VCF
  brass_score int Number of aberrant pairs contributing to the rearrangement group.
  strand1 [+-]    Strand of end in 'genomic' context - see table
  strand2 [+-]    Strand of end in 'genomic' context
  </code></pre>
   681: <p><a href="https://github.com/fritzsedlazeck/SURVIVOR" rel="nofollow noreferrer">SURVIVOR</a> has a subcommand to convert an SV vcf to bed, although I'm not sure if it's actual bedpe format.</p>
  
  <p>To install:</p>
  
  <pre><code>git clone https://github.com/fritzsedlazeck/SURVIVOR.git
  cd SURVIVOR/Debug
  make
  </code></pre>
  
  <p>Then:</p>
  
  <pre><code>./SURVIVOR vcftobed input.vcf <span class="math-container">$minSize $</span>maxSize output.bed
  </code></pre>
  
  <p>If you run this on your example file, you get:</p>
  
  <pre><code>$ ./SURVIVOR vcftobed foo.vcf 1 10000000000000000 bar.bed; cat bar.bed 
  chr1    1584528 1584528 chr1    1651069 1651069 11  ,   -   +   DUP
  </code></pre>
  