The intersect
command is the workhorse of the bedtools suite. It compares two or more BED/BAM/VCF/GFF
files and identifies all the regions in the genome where the features in the two files overlap (that is, share at least one base pair in common).
无参数直接输出overlap部分
-wa 输出有overlap的A文件的整个区间
-wb 输出有overlap的B文件的整个区间
-v 只输出A和B完全overlap的区间
-wo 输出overlap区间,只要有overlap就输出, 和不输入参数一样
-f 对于A文件,最小overlap的区间的比例,大于他保留,例如0.3
-F 对于B文件,最小overlap的区间的比例,大于他保留
-r 两个文件reciprocal的overlap比例,拷贝数矫正用这个, 需要和-f联用,-f指定比例
Many datasets of genomic features have many individual features that overlap one another (e.g. aligments from a ChiP seq experiment). It is often useful to just cobine the overlapping into a single, contiguous interval. The bedtools merge command will do this for you.
-d 指定两个要merge的区间之间的最大间隔大小(bp)