bedtools merge output interval different by 1 in each direction

[kszkop]

I have number of files in delimited format: chromosome start end . I would like to merge overlapping intervals between files, keeping option min distance between intervals to be merged. I cat all files , sorted and applied bedtools merge with option -d. All good, but the problem I have is that when interval is of length 1, the output from bedtools merge outputs it as +1 -1 interval. For example:
my input: chr 421 421
my output" chr 420 422

[tdelhomme]

I get the same problem.

bedtools v2.25.0

cat test.bed
chr12	25398284	25398284
chr12	25398285	25398285

bedtools merge -i test.bed
chr12	25398283	25398286

[ghuls]

This is probably because BED is a zero-based half open interval (first base of chromosome = 0, end coordinate is not included in the interval):

chr 421 421 ==> is a region of length 0, starts at base 422 (421 + 1) in the chromosome and ends before base 422

so your regions all have a length of 0 basepares.

If you have BED regions which have a length of at least 1 basepare, it works fine.

$ printf 'chr1\t421\t422\nchr1\t422\t423\n'
chr1	421	422
chr1	422	423

$ printf 'chr1\t421\t422\nchr1\t422\t423\n' | ./bedtools2-git/bin/bedtools merge -i -
chr1	421	423

[tdelhomme]

@mfoll

[mfoll]

Indeed:

BED starts are zero-based and BED ends are one-based.

http://bedtools.readthedocs.io/en/latest/content/overview.html#bed-starts-are-zero-based-and-bed-ends-are-one-based