How to understand Structural Variation in bedpe format?

Question

[Shicheng Guo]

Hi All,

How to understand the structural variation with bedpe format?

For example, the first one is duplication, how to know which region is duplicated ? how many duplicates happened?

what does start1 and end1 mean? why they are always having 1b difference?

chrom1  start1  end1    chrom2  start2  end2    sv_id   pe_support  strand1 strand2 svclass
1   10428600    10428601    1   10582238    10582239    SVMERGE93   80  -   +   DUP
1   26939174    26939175    1   27518317    27518318    SVMERGE102  89  +   -   DEL
1   29834388    29834389    1   33723647    33723648    SVMERGE100  107 -   -   t2tINV
1   29834417    29834418    1   33723675    33723676    SVMERGE101  87  +   +   h2hINV
1   32728334    32728335    1   32845969    32845970    SVMERGE99   33  -   +   DUP
1   78236345    78236346    1   78427706    78427707    SVMERGE98   71  +   -   DEL
1   151858704   151858705   13  44927717    44927718    SVMERGE151  75  -   +   TRA
1   151873175   151873176   1   183511505   183511506   SVMERGE152  41  +   -   DEL
1   151887225   151887226   13  44703672    44703673    SVMERGE163  65  -   -   TRA

Thanks.

I download these data from PCAWG website: https://dcc.icgc.org/releases/PCAWG/consensus_sv

Answer 1

[jxcao9812]

start1/end1 are the endpoints of confidence intervals of left breakpoints, and start2/end2 are the same for the right breakpoints