What it does
This is a wrapper for intersecBed.
Program: intersectBed (v2.13.3) Author: Aaron Quinlan (email@example.com) Summary: Report overlaps between two feature files.
intersectBed [OPTIONS] -a (bed/gff/vcf) -b (bed/gff/vcf)
|-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.|
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.
Only A features with overlap are reported.
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.
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)|
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
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.|