Merge overlapping intervals in a bed file containing different chromosomes

Question

[dzisis1986]

Hello I have a file test.bed like this :

    chr2    3300000 3499999 0   0.013255902570394
    chr3    300000  499999  0   0.015744466292456
    chr4    9400000 9599999 0   0.045555030342908
    chr5    1700000 1899999 0   0.013255902570394
    chr5    23900000    24099999    0   0.037583056937021
    chr5    3000000 3199999 0   2.62328977303342E-06
    chr5    3100000 3299999 0   1.61951552785474E-08
    chr5    3200000 3399999 0   0.001461420574531
    chr5    3700000 3899999 0   0.013255902570394
    chr5    3800000 3999999 0   0.013255902570394

I would like to merge intervals that are overlapping and create a new merged.bed file like this :

chr2    3300000 3499999
chr3    300000  499999
chr4    9400000 9599999
chr5    1700000 1899999
chr5    3000000  3399999
chr5    3700000  3999999
chr5    23900000    24099999

Answer 1

[Pierre Lindenbaum]

sort and use bedtools merge

[dzisis1986]

I already did this but something is wrong with sort , maybe the fact that there are different chr and when i use bedtools merge i have an error like :

Error: Sorted input specified, but the file sorted.bed has the following out of order record
chr5    3700000 3899999 0   0.013255902570394

[Pierre Lindenbaum]

I already did this

you should have told us

maybe the fact that there are different chr an

how did you sort the file. what was the command line ?

[dzisis1986]

i used different sort command like sortBed -i and also sort -n -k1.11 -nk2,2 . but still the same problem !

[Pierre Lindenbaum]

sort -t $'\t' -k1,1 -k2,2n in.bed | bedtools merge > out.bed