**-s** Force strandedness. That is, only features in A are only counted towards coverage in B if they are the same strand. *By default, this is disabled and coverage is counted without respect to strand*.
**-hist** Report a histogram of coverage for each feature in B as well as a summary histogram for _all_ features in B.
| Output (tab delimited) after each feature in B:
| 1) depth
| 2) # bases at depth
| 3) size of B
| 4) % of B at depth
**-d** Report the depth at each position in each B feature. Positions reported are one based. Each position and depth follow the complete B feature.
**-split** Treat "split" BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR "N" and "D" operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12).
**-a** BAM/BED/GFF/VCF file "A". Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe.
**-b** One or more BAM/BED/GFF/VCF file(s) "B". Use "stdin" if passing B with a UNIX pipe.
**NEW!!!**: -b may be followed with multiple databases and/or wildcard (*) character(s).
**-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b <BAM> | bedtools intersect -abam stdin -b genes.bed. **Note**: no longer necessary after version 2.19.0
**-hist** | Report a histogram of coverage for each feature in A as well as a summary histogram for _all_ features in A.
| Output (tab delimited) after each feature in A:
| 1) depth
| 2) # bases at depth
| 3) size of A
| 4) % of A at depth
**-d** Report the depth at each position in each A feature. Positions reported are one based. Each position and depth follow the complete A feature.
**-counts** Only report the count of overlaps, don't compute fraction, etc. Restricted by -f and -r.
**-f** Minimum overlap required as a fraction of A. 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.
**-s** Force "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 (i.e., having an "N" CIGAR operation) or BED12 entries as distinct BED intervals.
**-sorted** For very large B files, invoke a "sweeping" algorithm that requires position-sorted (e.g., ``sort -k1,1 -k2,2n`` for BED files) input. When using -sorted, memory usage remains low even for very large files.
**-g** Specify a genome file the defines the expected chromosome order in the input files for use with the ``-sorted`` option.
**-header** Print the header from the A file prior to results.
**-sortout** When using *multiple databases* (`-b`), sort the output DB hits for each record.
**-nobuf** Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time.
**-iobuf** Follow with desired integer size of read buffer. Optional suffixes `K/M/G` supported. **Note**: currently has no effect with compressed files.
