3
$\begingroup$

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
$\endgroup$
  • $\begingroup$ Do you really mean bedpe? 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? $\endgroup$ – terdon Jul 5 at 23:59
  • $\begingroup$ @terdon I've edited the question for clarity $\endgroup$ – EB2127 Jul 6 at 1:41
  • 1
    $\begingroup$ 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? $\endgroup$ – terdon Jul 6 at 11:20
2
$\begingroup$

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
$\endgroup$
  • $\begingroup$ 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. $\endgroup$ – terdon Jul 7 at 12:09
  • $\begingroup$ 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. $\endgroup$ – Wouter De Coster Jul 7 at 15:40
  • 1
    $\begingroup$ It's a question of what is considered an answer on the SE platform. 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. $\endgroup$ – terdon Jul 7 at 15:47
  • $\begingroup$ 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? $\endgroup$ – EB2127 Jul 7 at 18:30
  • $\begingroup$ 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. $\endgroup$ – terdon Jul 7 at 18:55

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