The gff format is confusing (which is my fault, since at the time there was no bed format). The bed format only has the data in different order, and 0-based. The bed format is defined here, and is especially useful since there are a ton of tools that can handle bed files, most notably BEDTOOLS.
The
gffformat is confusing (which is my fault, since at the time there was nobedformat). Thebedformat only has the data in different order, and 0-based. Thebedformat is defined here, and is especially useful since there are a ton of tools that can handle bed files, most notably BEDTOOLS.http://genome.ucsc.edu/FAQ/FAQformat.html#format1
You can change from
gffformat tobedthrough:awk '{print $1"\t"$3"\t"$4"\t"$2}' grape.gff >grape.bed