The breaks.bedpe file has 10-columns that represent the genomic coordinates of the partner sequences involved in a structural variant.
“chr1” is the chromosome ID for the first partner
“x1” is the starting coordinate of the first partner
“x2” is the end coordinate of the first partner
“chr2” is the chromosome ID for the second partner
“y1” is the starting coordinate of the second partner
“y2” is the end coordinate of the second partner
This format is different from traditional SV calls which specify a precise break point and is due to the resolution of the SV call from hic_breakfinder that can be found in the “resolution” column.
The “strand1” and “strand2” columns indicate which corner of the square SV call is likely to contain the breakpoint. A “+” indicates that the breakpoint is predicted near the end coordinate (3’) and a “-“ predicts that the breakpoint is predicted at the start coordinate (5’) for a given partner.
“-logP” is the -log scaled p-value of the SV call.