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  • 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.



    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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