6.3.3. Data conversionΒΆ

Wrapper scripts around the convert2bed utility quickly convert a variety of common genomic data types to BED with no loss of information. In using these tools, you can easily prepare data from these formats for use with core BEDOPS tools, whether VCF, GFF/GTF/GVF, BAM/SAM, PSL (Blat), RepeatMasker annotation output, etc.

Some other formats not covered here can be converted with, for instance, the UCSC Kent toolset (e.g., altGraphX, bigWig, bigBed, etc.). Just remember to use the sort-bed utility to prepare BED output from external programs for use with BEDOPS core tools.