BED file handling software : bedtools, BEDOPS

bedtools: a powerful toolset for genome arithmetic

http://bedtools.readthedocs.io/en/latest/#

bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit¶

https://bedops.readthedocs.io/en/latest/index.html

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

Data conversion

6.3.3.2. bam2bed

6.3.3.5. gff2bed

6.3.3.6. gtf2bed

6.3.3.10. sam2bed

6.3.3.11. vcf2bed

6.3.3.12. wig2bed