Two adjacent sites were not annotated by gene features using bedtools intersect.

[Chentao Yang]

Hello,

I am using bedtools intersect program to annotate genome variants.

I found a case that is not like what I expected, I wonder is there anything I misunderstood.

here is an example,

a.bed

chr1 10 11

b.bed

chr1 2 10   A

chr1 11 15   B

command:

bedtools intersect -a a.bed  -b  b.bed -wa -wb -loj

result:
chr1 10 11 . -1 -1

I thought the result was like fellows because they both have a 1-bp overlap with gene features.
chr1 10 11  chr1 2 10   A

chr1 10 11  chr1 11 15   B

P.S. the version I used is v2.27.1

[Aaron Quinlan]

Hi Chentao,

These adjacent intervals do not overlap in the zero-based, half-open coordinate system that BED format uses.

https://www.biostars.org/p/84686/

Aaron

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