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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.
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:
As are these:
Bug fixes
1. Increased the precision of the output from groupBy.
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
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.