BEDTools version 2.10.0

quinlana · 09-21-2010, 05:25 PM

Hi all,
I just posted version 2.10.0. Below are the highlights including a new tool and some useful new features.

http://code.google.com/p/bedtools/

Best,
Aaron

New tools
1. annotateBed. Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types via a single command. As an example, the following will annotate the fraction of the variants in variants.bed that are covered by genes, conserved regions and know variation, respectively.

Code:

$ annotateBed -i variants.vcf -files genes.bed conserv.bed known_var.vcf

New features

1. New frequency operations (freqasc and freqdesc) added to groupBy. These operations report a histogram of the frequency that each value is observed in a given column.

2. Support for writing uncompressed bam with the -ubam option.

3. Shorthand arguments for groupBy (-g = -grp, -c = -opCols, -o = -opCols).

4. In addition, all BEDTools that require only one main input file (the -i file) will assume that input is coming from standard input if the -i parameter is ignored. For example, the following are equivalent:

Code:

$ cat snps.bed | sortBed –i stdin
$ cat snps.bed | sortBed

As are these:

Code:

$ cat data.txt | groupBy -i stdin -g 1,2,3 -c 5 -o mean
$ cat data.txt | groupBy -g 1,2,3 -c 5 -o mean

Bug fixes
1. Increased the precision of the output from groupBy.

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09-21-2010, 05:25 PM	#1
quinlana Senior Member Location: Charlottesville Join Date: Sep 2008 Posts: 117	BEDTools version 2.10.0 Hi all, I just posted version 2.10.0. Below are the highlights including a new tool and some useful new features. http://code.google.com/p/bedtools/ Best, Aaron New tools 1. annotateBed. Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types via a single command. As an example, the following will annotate the fraction of the variants in variants.bed that are covered by genes, conserved regions and know variation, respectively. Code: $ annotateBed -i variants.vcf -files genes.bed conserv.bed known_var.vcf New features 1. New frequency operations (freqasc and freqdesc) added to groupBy. These operations report a histogram of the frequency that each value is observed in a given column. 2. Support for writing uncompressed bam with the -ubam option. 3. Shorthand arguments for groupBy (-g = -grp, -c = -opCols, -o = -opCols). 4. In addition, all BEDTools that require only one main input file (the -i file) will assume that input is coming from standard input if the -i parameter is ignored. For example, the following are equivalent: Code: $ cat snps.bed \| sortBed –i stdin $ cat snps.bed \| sortBed As are these: Code: $ cat data.txt \| groupBy -i stdin -g 1,2,3 -c 5 -o mean $ cat data.txt \| groupBy -g 1,2,3 -c 5 -o mean Bug fixes 1. Increased the precision of the output from groupBy.