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

LauraSmith · 02-15-2012, 09:35 AM

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 · 02-16-2012, 06:19 AM

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 · 02-23-2012, 01:59 AM

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 · 05-21-2013, 11:54 AM

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.

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02-15-2012, 09:35 AM	#1
LauraSmith Junior Member Location: SAN FRANCISCO Join Date: Dec 2011 Posts: 4	Is there a BED file format validator? Does a BED file have to be sorted position? 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

05-21-2013, 11:54 AM	#4
AlexReynolds Member Location: Seattle, WA Join Date: Feb 2013 Posts: 45	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. Last edited by AlexReynolds; 05-22-2013 at 06:32 PM.

02-16-2012, 06:19 AM	#2
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	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.

02-23-2012, 01:59 AM	#3
maasha Senior Member Location: Denmark Join Date: Apr 2009 Posts: 153	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