Comparing two files with overlapping regions and get their associated information
You can use bedtools intersect and cut the results:

$ cat file1.bed
chr1    12048   177033  DUP FALSE   -1  22  24
chr1    12048   89237   DUP FALSE   12  10  -1
chr1    2985712 3355300 DEL TRUE    2   2   2

$ cat file2.gtf
chr1    22013   41670   gene_id "ENSG00000160075.10"
chr1    22013   41670   gene_id "ENSG00000160075.10"
chr1    2985732 3355185 gene_id "ENSG00000142611.12"

$ bedtools intersect -a file2.gtf -b file1.bed -wb | cut -f 1-4,8-11
chr1    22013   41670   gene_id "ENSG00000160075.10"    DUP FALSE   12  10
chr1    22013   41670   gene_id "ENSG00000160075.10"    DUP FALSE   -1  22
chr1    2985732 3355185 gene_id "ENSG00000142611.12"    DEL TRUE    2   2