Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-07T12:09:28.817Z
Answers.Text: Could you edit your answer and add this command's name and how to execute it? As it stands, this is kind of more of a comment than an answer.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-07T15:40:17.310Z
Answers.Text: Feel free to move it to a comment then. I consider the documentation of the tool sufficient and clear, and do not believe that copy-pasting that usage information is beneficial, as it might get outdated while the official documentation shouldn't.
Answers.UserDisplayName: Wouter De Coster
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-07T15:47:46.840Z
Answers.Text: It's a question of [what is considered an answer on the SE platform](https://meta.stackexchange.com/q/225370/203101). This seems like a good answer, but we really want the relevant information to be _here_ in case the link goes stale and to be able to have the relevant details here. You're linking to the docs, so if they change and your instructions become obsolete, the docs will still be there. In the meantime, however, this is not actually giving us enough info to know how to use it and that's a shame.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-07T18:30:25.850Z
Answers.Text: Hi @terdon, thanks for the edits. "However, this isn't a bedpe file, so it looks like it isn't what the OP was asking for". That looks pretty close to a BEDPE, right? What is the difference you see, besides the file extension?
Answers.UserDisplayName: EB2127
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-07T18:55:17.957Z
Answers.Text: Whoops, my bad! It is indeed a bedpe and not a bed. I had managed to miss the second set of coordinates, sorry! However, it doesn't seem to be right for what the OP wants since that's just repeating the start position two times and then the end position another two times. Have a look at the blog post the OP linked to for what they seem to be looking for.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-07T09:30:24.180Z
Answers.LastActivityDate: 2019-07-07T15:53:37.363Z
Answers.LastEditDate: 2019-07-07T15:53:37.363Z
Answers.UserDisplayName: Wouter De Coster
Body: <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-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 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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-05T23:59:57.053Z
Comments.Text: Do you really mean [bedpe](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format)? I may be missing something, but what would converting a vcf to bedpe even mean? Bedpe is normally used to described paired sequences, usually primers. What would converting a VCF to bedpe entail? Could you maybe [edit] your question and give an example of a minimal VCF and what it would look like as bedpe?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-06T01:41:48.443Z
Comments.Text: @terdon I've edited the question for clarity
Comments.UserDisplayName: EB2127
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-06T11:20:40.930Z
Comments.Text: Thanks! That makes it much clearer. I don't really see how you'd represent deletions, but if the LUMPY folks are doing it, I guess it must be possible. Did you try `vftobedpe` from svtools?
Comments.UserDisplayName: terdon
Tags: <vcf><structural-variation>
Title: Is there a standard tool used to convert a VCF to a BEDPE?
ThreadText: # Is there a standard tool used to convert a VCF to a BEDPE?
  
  (Asked by: username_0 on 2019-07-05)
  
  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-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 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
  
  ```
  
  **Tags:** vcf, structural-variation
  
  > **Comments:**
  > **username_1**: Do you really mean [bedpe](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format)? I may be missing something, but what would converting a vcf to bedpe even mean? Bedpe is normally used to described paired sequences, usually primers. What would converting a VCF to bedpe entail? Could you maybe [edit] your question and give an example of a minimal VCF and what it would look like as bedpe?  
  > **username_0**: @username_1 I've edited the question for clarity  
  > **username_1**: Thanks! That makes it much clearer. I don't really see how you'd represent deletions, but if the LUMPY folks are doing it, I guess it must be possible. Did you try `vftobedpe` from svtools?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-07-07. Score: 3
  
  [SURVIVOR](https://github.com/fritzsedlazeck/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
  
  ```
  
  > **Comments:**
  > **username_1**: Could you edit your answer and add this command's name and how to execute it? As it stands, this is kind of more of a comment than an answer.  
  > **username_2**: Feel free to move it to a comment then. I consider the documentation of the tool sufficient and clear, and do not believe that copy-pasting that usage information is beneficial, as it might get outdated while the official documentation shouldn't.  
  > **username_1**: It's a question of [what is considered an answer on the SE platform](https://meta.stackexchange.com/q/225370/203101). This seems like a good answer, but we really want the relevant information to be _here_ in case the link goes stale and to be able to have the relevant details here. You're linking to the docs, so if they change and your instructions become obsolete, the docs will still be there. In the meantime, however, this is not actually giving us enough info to know how to use it and that's a shame.  
  > **username_0**: Hi @username_1, thanks for the edits. "However, this isn't a bedpe file, so it looks like it isn't what the OP was asking for". That looks pretty close to a BEDPE, right? What is the difference you see, besides the file extension?  
  > **username_1**: Whoops, my bad! It is indeed a bedpe and not a bed. I had managed to miss the second set of coordinates, sorry! However, it doesn't seem to be right for what the OP wants since that's just repeating the start position two times and then the end position another two times. Have a look at the blog post the OP linked to for what they seem to be looking for.  
  
  ---
  
  