What it does

This is a wrapper for intersecBed.

Program: intersectBed (v2.13.3) Author: Aaron Quinlan (aaronquinlan@gmail.com) Summary: Report overlaps between two feature files.

Usage:

intersectBed [OPTIONS] -a (bed/gff/vcf) -b (bed/gff/vcf)

Options::

-abam	The A input file is in BAM format. Output will be BAM as well.
-ubam	Write uncompressed BAM output. Default is to write compressed BAM.
-bed	When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam.
-wa	Write the original entry in A for each overlap.
-wb	Write the original entry in B for each overlap. - Useful for knowing _what_ A overlaps. Restricted by -f and -r.
-wo	Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlaps restricted by -f and -r. System Message: ERROR/3 (<string>, line 31) Unexpected indentation. Only A features with overlap are reported.
-wao	Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlapping features restricted by -f and -r. System Message: ERROR/3 (<string>, line 36) Unexpected indentation. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.
-u	Write the original A entry _once_ if _any_ overlaps found in B. - In other words, just report the fact >=1 hit was found. - Overlaps restricted by -f and -r.
-c	For each entry in A, report the number of overlaps with B. - Reports 0 for A entries that have no overlap with B. - Overlaps restricted by -f and -r.
-v	Only report those entries in A that have _no overlaps_ with B. - Similar to "grep -v" (an homage).
-f	Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
-r	Require that the fraction overlap be reciprocal for A and B. - In other words, if -f is 0.90 and -r is used, this requires System Message: ERROR/3 (<string>, line 56) Unexpected indentation. that B overlap 90% of A and A _also_ overlaps 90% of B.
-s	Require same strandedness. 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.
-split	Treat "split" BAM or BED12 entries as distinct BED intervals.

-sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input

NOTE: this will trust, but not enforce that data is sorted. Caveat emptor.