BEDTools: Unexpected file format. Please use tab-delimited BED, GFF, or VCF.

[id0]

I am using BEDTools and getting the following error:

Unexpected file format.  Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?

I had a GFF file and figured maybe there is indeed a problem, so I converted it to a 3-column BED file just to be safe. The BED file did not work either.

I searched around for this error and it's usually caused by non-unix newlines or non-tab separators. My file does not have either of those issues.

Here are the first few lines of the BED file:

chr1	3214482	3216968
chr1	3421702	3421901
chr1	3670552	3671498
chr1	4290846	4293012
chr1	4343507	4350091

Any idea what may be causing this error?

[GenoMax]

Check the bed file using the following command to make sure there are no unexpected characters.

$ cat -e filename.bed | more

or

$ cat -A filename.bed | more

The tab characters are displayed as "^I" (at least on CentOS).

[id0]

Check the bed file using the following command to make sure there are no unexpected characters and the file is indeeded tab limited.

$ cat -e filename.bed | more

I already did that. No unexpected characters.

[GenoMax]

Are you getting the error even with a small subset like the one you pasted above?

[id0]

Used different files and small subsets and still getting the same problem.

Supposedly, the problem is at line 1, but there is really nothing wrong with it as far as I can tell.

[GenoMax]

Not sure which exact bedtools program you need but perhaps bedops (http://code.google.com/p/bedops/) could provide an alternative.

[id0]

I am using coverageBed. I just wanted to quickly get coverage at specific regions.

I have a valid BED file. Why is BEDTools disagreeing?

[GenoMax]

Have you used this copy of bedtools successfully before?

[id0]

No. Unfortunately I just got BEDTools.

It compiled and it seems to be running okay for the most part. I assume if there was a problem with BEDTools, it wouldn't launch in the first place or produce some other lower-level error first.

[Heisman]

Create a file with vim and then type the following (with tabs):

chr1 500 1000
chr1 700 1200

and try to use "mergeBed" on it and see if that works.

[id0]

Create a file with vim and then type the following (with tabs):

chr1 500 1000
chr1 700 1200

and try to use "mergeBed" on it and see if that works.

mergeBed works on that example. It also works on other BED files.

coverageBed does not work on any of the files.

This is very confusing.

[wadachi]

How about checking "new line characters"?

if you make your .bed files on Windows, new line characters should be set \r\n.
whereas Unix/Linux uses only \r, so the excess \n may make BEDTools confused.

to justify this, choose line end character of Unix/Linux in the selection pulldown in your text editor's "save as ..." dialogue. (in my case, gedit in Ubuntu).

hope this works!

[inesdesantiago]

You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html

[jshaik]

use dos2unix command in linux to convert your bed file to a file that is acceptable by bedtools. This happens as the windows and linux have different new line characters

[Armin_P]

I was facing the same problem. One of my files was a bam file and the other gff3/bed (I do not know if you have a bam file). Anyways, I used 'bedtools coverage' with the -abam option instead of -a and provided my bam file there. -b was then the gff3 or .bed (I tried both) and it worked!