bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.
subtractBed [OPTIONS] -a
-f Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
-F Minimum overlap required as a fraction of B. Default is 1E-9 (i.e., 1bp).
-r Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
-e Require that the minimum fraction be satisfied for A _OR_ B. In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied.**-s** Force “strandednessâ€. That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
-S Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
-A Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed.
-N Same as -A except when used with -f, the amount is the sum of all features (not any single feature).