I am trying to add the gene_name to a bed file and I think the method I used below is using the gene_id instead. Is it possible to get the gene_name and maybe exon_number? Thank you

1. wget ftp://ftp.sanger.ac.uk/pub/gencode/release_21/gencode.21.annotation.gtf.gz

2.

gunzip --stdout gencode.v21.annotation.gtf.gz \
    | gtf2bed - \
    | grep "exon" \
    > gencode.exons.bed

3. bedmap --echo --echo-map-id-uniq epilepsy70_medex_edit.bed gencode.exons.bed > output.bed

genecode_exons.bed

chr1 11868 12227 ENSG00000223972.5 . + HAVANA exon . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; transcript_support_level "1"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

output.bed (as of now)

chr1 43408884 43409004
|
chr1    43424253    43424373
|ENSG00000198198.11
chr1    154540492   154540612
|
chr1    154541927   154542093
|ENSG00000163239.10

epilepsy70_medex_edit.bed

chr1    40539722    40539865
chr1    40542489    40542609
chr1    40544221    40544341
chr1    40546054    40546174
chr1    40555071    40555194