bedtool sort not working properly?

[robi...@gmail.com]

Hi,

I'm trying to sort and then merge a bed file. But the sortBed didn't working as expected, see below:

cat test.bed:

chr2 180036938 180037000

chr2 180037383 180037502

chr2 180037384 180037384

chr2 180037383 180037488

chr2 180037383 180037502

chr2 180037634 180038187

chr2 180038065 180038187

sortBed -i test.bed > test.sorted.bed

cat test.sorted.bed:

chr2 180036938 180037000

chr2 180037383 180037502

chr2 180037384 180037384

chr2 180037383 180037488

chr2 180037383 180037502

chr2 180037634 180038187

chr2 180038065 180038187

mergeBed -i test.sorted.bed

Error: Sorted input specified, but the file test.sorted.bed has the following out of order record

chr2 180037383 180037488

Could you please help me solve this? 

Thank you!

Robin

[Aaron Quinlan]

Sorry for this, It looks like the sort tool does not handle zero-length BED records correctly.

I would recommend sorting with the following until we can drop in a fix. Moreover, it is probably better to just use UNIX sort anyway given that it will scale much more favorably than bedtools sort.

sort -k1,1 -k2,2n test.bed > test.sorted.bed

Best,

Aaron 

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