Closed:conversion of gff to bed file

Question

[evafinegan]

Hello,

I want to convert a gff file to a bed file. I used:

gff2bed < sample.gff > sample.bed

I want to keep four columns in the output file in the order of gene_name chromosome start_position end_position However, after the conversion and some manual steps to keep first four columns and reordering the columns, I am getting same names multiple times with same positions such as:

V_06g024400.1   Vch06   21881   22007
V_06g024400.1.1 Vch06   21881   22007
V_06g024400.1.1:cds Vch06   21881   22007
V_06g024400.1.1:exon:2  Vch06   21881   22007

I also want to add column names as gene_name chromosome start_position end_position. Is there any way to keep unique positions only and to avoid these manual changes to the file in order to get the desired output. Thank you!