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  • bedtools intersect -f -F -r behavior

    Hello, I am using bedtools intersect and I'm failing to reproduce one of the examples in the documentation, bedtools intersect

    I am using bedtools v2.25.0

    In section "-r, and -f Requiring reciprocal minimal overlap fraction", the very simple example provided there is:
    $ cat A.bed
    chr1 100 200

    $ cat B.bed
    chr1 130 201
    chr1 130 200000

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -r -wa -wb
    chr1 100 200 chr1 130 201


    Well, in my case, when I try to force reciprocal overlap, the behavior is not what I expected. My output is:

    $ cat A.bed
    chr1 100 200

    $ cat B.bed
    chr1 130 201
    chr1 130 200000

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -wa -wb
    chr1 100 200 chr1 130 201
    chr1 100 200 chr1 130 200000

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -r -wa -wb
    chr1 100 200 chr1 130 201
    chr1 100 200 chr1 130 200000

    Last output is different from the example. -r seems to be ignored, I only get the expected reciprocal result manually using -F:

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -F 0.50 -wa -wb
    chr1 100 200 chr1 130 201

    Using -f and -r should be the same than using -f and -F, right?
    Does anyone have any idea of what I'm missing?

    Thank you so much for your feedback!

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