bedtools is a powerful toolset for genome arithmetic. Version: v2.26.0 About: developed in the quinlanlab.org and by many contributors worldwide. Docs: http://bedtools.readthedocs.io/ Code: https://github.com/arq5x/bedtools2 Mail: https://groups.google.com/forum/#!forum/bedtools-discuss Usage: bedtools <subcommand> [options] The bedtools sub-commands include: [ Genome arithmetic ] intersect Find overlapping intervals in various ways. window Find overlapping intervals within a window around an interval. closest Find the closest, potentially non-overlapping interval. coverage Compute the coverage over defined intervals. map Apply a function to a column for each overlapping interval. genomecov Compute the coverage over an entire genome. merge Combine overlapping/nearby intervals into a single interval. cluster Cluster (but don't merge) overlapping/nearby intervals. complement Extract intervals _not_ represented by an interval file. shift Adjust the position of intervals. subtract Remove intervals based on overlaps b/w two files. slop Adjust the size of intervals. flank Create new intervals from the flanks of existing intervals. sort Order the intervals in a file. random Generate random intervals in a genome. shuffle Randomly redistrubute intervals in a genome. sample Sample random records from file using reservoir sampling. spacing Report the gap lengths between intervals in a file. annotate Annotate coverage of features from multiple files. [ Multi-way file comparisons ] multiinter Identifies common intervals among multiple interval files. unionbedg Combines coverage intervals from multiple BEDGRAPH files. [ Paired-end manipulation ] pairtobed Find pairs that overlap intervals in various ways. pairtopair Find pairs that overlap other pairs in various ways. [ Format conversion ] bamtobed Convert BAM alignments to BED (& other) formats. bedtobam Convert intervals to BAM records. bamtofastq Convert BAM records to FASTQ records. bedpetobam Convert BEDPE intervals to BAM records. bed12tobed6 Breaks BED12 intervals into discrete BED6 intervals. [ Fasta manipulation ] getfasta Use intervals to extract sequences from a FASTA file. maskfasta Use intervals to mask sequences from a FASTA file. nuc Profile the nucleotide content of intervals in a FASTA file. [ BAM focused tools ] multicov Counts coverage from multiple BAMs at specific intervals. tag Tag BAM alignments based on overlaps with interval files. [ Statistical relationships ] jaccard Calculate the Jaccard statistic b/w two sets of intervals. reldist Calculate the distribution of relative distances b/w two files. fisher Calculate Fisher statistic b/w two feature files. [ Miscellaneous tools ] overlap Computes the amount of overlap from two intervals. igv Create an IGV snapshot batch script. links Create a HTML page of links to UCSC locations. makewindows Make interval "windows" across a genome. groupby Group by common cols. & summarize oth. cols. (~ SQL "groupBy") expand Replicate lines based on lists of values in columns. split Split a file into multiple files with equal records or base pairs. [ General help ] --help Print this help menu. --version What version of bedtools are you using?. --contact Feature requests, bugs, mailing lists, etc.