更详细的介绍，移步 https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html
& https://blog.csdn.net/qazplm12_3/article/details/79797594
bedtools: flexible tools for genome arithmetic and DNA sequence analysis.
usage: bedtools <subcommand> [options]
The bedtools sub-commands include:
[ Genome arithmetic ]
1 intersect ：Find overlapping intervals in various ways.
求区域之间的交集，可以用来注释peak，计算reads比对到的基因组区域不同样品的peak之间的peak重叠情况。
2 window ：Find overlapping intervals within a window around an interval.
3 closest ：Find the closest, potentially non-overlapping interval. 寻找最近但可能不重叠的区域
4 coverage ：Compute the coverage over defined intervals. 计算区域覆盖度
5 map ：Apply a function to a column for each overlapping interval.
6 genomecov ：Compute the coverage over an entire genome.
7 merge ：Combine overlapping/nearby intervals into a single interval. 合并重叠或相接的区域
8 cluster ：Cluster (but don't merge) overlapping/nearby intervals.
9 complement ：Extract intervals not represented by an interval file. 获得互补区域
10 subtract ：Remove intervals based on overlaps b/w two files. 计算区域差集
11 slop ：Adjust the size of intervals. 调整区域大小，如获得转录起始位点上下游3 K的区域
12 flank ：Create new intervals from the flanks of existing intervals.
13 sort ：Order the intervals in a file. 排序，部分命令需要排序过的bed文件
14 random ：Generate random intervals in a genome. 获得随机区域，作为背景集
15 shuffle ：Randomly redistrubute intervals in a genome. 根据给定的bed文件获得随机区域，作为背景集
16 sample ：Sample random records from file using reservoir sampling.
17 spacing ：Report the gap lengths between intervals in a file.
18 annotate ：Annotate coverage of features from multiple files.
[ Multi-way file comparisons ]
19 multiinter ：Identifies common intervals among multiple interval files.
20 unionbedg ：Combines coverage intervals from multiple BEDGRAPH files.
[ Paired-end manipulation ]
21 pairtobed ：Find pairs that overlap intervals in various ways.
22 pairtopair ：Find pairs that overlap other pairs in various ways.
[ Format conversion ]
23 bamtobed ：Convert BAM alignments to BED (& other) formats.
24 bedtobam ：Convert intervals to BAM records.
25 bamtofastq ：Convert BAM records to FASTQ records.
26 bedpetobam ：Convert BEDPE intervals to BAM records.
27 bed12tobed6 ：Breaks BED12 intervals into discrete BED6 intervals.
[ Fasta manipulation ]
28 getfasta ：Use intervals to extract sequences from a FASTA file. 提取给定位置的FASTA序列
29 maskfasta ：Use intervals to mask sequences from a FASTA file.
30 nuc ：Profile the nucleotide content of intervals in a FASTA file.
[ BAM focused tools ]
31 multicov ：Counts coverage from multiple BAMs at specific intervals.
32 tag ：Tag BAM alignments based on overlaps with interval files.
[ Statistical relationships ]
33 jaccard ：Calculate the Jaccard statistic b/w two sets of intervals. 计算数据集相似性
34 reldist ：Calculate the distribution of relative distances b/w two files.
35 fisher ：Calculate Fisher statistic b/w two feature files.
[ Miscellaneous tools ]
36 overlap ：Computes the amount of overlap from two intervals.
37 igv ：Create an IGV snapshot batch script. 用于生成一个脚本，批量捕获IGV截图
38 links ：Create a HTML page of links to UCSC locations.
39 makewindows ：Make interval "windows" across a genome. 把给定区域划分成指定大小和间隔的小区间 (bin)
40 groupby ：Group by common cols. & summarize oth. cols. (~ SQL "groupBy") 分组结算，不只可以用于bed文件。
41 expand ：Replicate lines based on lists of values in columns.
42 split ：Split a file into multiple files with equal records or base pairs.
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