Is there a BED file format validator? Does a BED file have to be sorted position?

[LauraSmith]

Hi Everyone,

I have 2 questions and would very much appreciate anyone's input:

1. Is there a BED file format validator? A tool or a java package perhaps available online to download?


2. Does a BED file have to be sorted by chromosome and position starting from the first line? I checked the UCSC Genomic browser website for BED file format specification and there doesn't seem to be a requirement for this, but wanted to double check here.

Thank you,
Laura

[mgogol]

1) Not that I know of. Try to upload it to UCSC?

2) No. Unless you're trying to do something with it that expects it to be sorted. If you need to sort, something like sort -k1,1 -k2,2n file.bed should do.

[maasha]

Using read_bed from Biopieces (www.biopieces.org) there is a -C switch that checks integrity:

http://code.google.com/p/biopieces/wiki/read_bed

[AlexReynolds]

If you want to validate coordinates, the BEDOPS bedops application can do this, using the --everything and --ec operators:

$ bedops --ec --everything myData.bed 1> /dev/null
...

If any problems with chromosome name or coordinates are found, the details will be printed to standard error; in this example, we direct standard output to /dev/null as we're only interested in finding and reporting errors.