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Old 08-15-2017, 08:07 AM   #1
pepeluisrr
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Location: Spain

Join Date: Jan 2017
Posts: 1
Default 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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