Finding overlapping regions in two file along with their associated information

Question

[BAGeno]

Hi,

I have two file in which there are chromosomes positions and other information. I want to find their overlapping regions for this purpose I used bedtools. And I got overlapping coordinates between both files. Now I want file in which I have other information from both files associated with overlapping regions. Here is sample of both files.

File 1

contig  start   end size    type    bi-allelic  S1  S2  S3
chr1    12048   177033  164985  DUP FALSE   -1  22  24
chr1    12048   89237   77189   DUP FALSE   12  10  -1
chr1    53897994 53905803   7809    DEL TRUE    2   2   2

File 2

chr1    901877  911245  gene_id "ENSG00000187583.6"; transcript_id "ENSG00000187583.6"; gene_type "protein_coding"; g                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
chr1    1477053 1510249 gene_id "ENSG00000160075.10"; transcript_id "ENSG00000160075.10"; gene_type "protein_coding";                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
chr1    2985732 3355185 gene_id "ENSG00000142611.12"; transcript_id "ENSG00000142611.12"; gene_type "protein_coding";

I want type bi-allelic and sample column from file 1 and gene id column from file 2 along with regions. Can any one has idea how to do this?