I'm having trouble with Bedtools Intersect. It is not reporting overlap when all of feature A is within feature B. 

Command:

    bedtools intersect -a File1.bed -b File2.gff -wao -f 0.90 -sorted > Out.file 

Out.file: 

    VMNF01000005.1	484754	484980	.	.	+	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000005.1	484754	484980	.	.	+	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000005.1	484754	484980	.	.	+	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000005.1	484754	484980	.	.	-	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000007.1	6294425	6294650	.	.	-	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000007.1	6294425	6294650	.	.	-	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000007.1	6294425	6294650	.	.	-	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000007.1	6294425	6294650	.	.	+	.	.	.	-1	-1	.	.	.	.	0
    VMNF01000008.1	1441418	1441616	.	.	-	.	.	.	-1	-1	.	.	.	.	0


When I search manually, all of feature A sits within feature B. 

![Image of overlap when viewed in Artemis. Feature A (pink and yellow highlighted region within circle) sits within feature B (red highlighted region).][1]

Can anybody please explain where I have gone wrong? 

Bedtools version: bedtools v2.29.2

  [1]: https://i.ibb.co/gy5x7V5/Artemis-VMNF-Promoter-in-red-mimp-in-pink.png
I will leave this for those who may be interested - the issue was that the scaffolds/contigs had a slight difference in the names between the .bed file and the .gff file. The .bed file included the suffix ".1". After adding ".1" to the scaffold/contig names in File2.gff, both bedtools intersect and bedmap worked. 

E.g.

    => File1.bed <==
    VMNF01000005.1 482754 486980 . . +
    VMNF01000005.1 482754 486980 . . +

    ==> File2.gff <==
    VMNF01000002 GenBank PROMOTER 1 34 . + 1 ID=FocTR4_00017231;Name=FocTR4_00017231
    VMNF01000002 GenBank PROMOTER 4227 5039 . - 1 ID=FocTR4_00017232;Name=FocTR4_00017232
