Bedtools is a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General 
Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.
The following are examples of common questions that one can address with BEDTools.
- Intersecting two BED files in search of overlapping features.
- Culling/refining/computing coverage for BAM alignments based on genome features.
- Merging overlapping features.
- Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
- Calculating the depth and breadth of sequence coverage across defined “windows” in a genome.
- Screening for overlaps between “split” alignments and genomic features.
BEDTools support a wide range of operations for interrogating and manipulating genomic features. The folowing tools available in the bedTool suite (tools that support BAM file are indicated).
IntersectBed – Returns overlapping features between two BED/GFF/VCF files (Also supports BAM format as input and output).
WindowBed – Returns overlapping features between two BED/GFF/VCF files within a “window” (Also supports BAM format as input and output).
ClosestBed – Returns the closest feature to each entry in a BED/GFF/VCF file.
CoverageBed – Summarizes the depth and breadth of coverage of features in one BED/GFF file (e.g., aligned reads) relative to another (e.g., user-defined windows) (Also supports BAM format as input and output).
GenomeCoverageBed – Histogram or a “per base” report of genome coverage (Also supports BAM format as input and output).
PairToBed – Returns overlaps between a BEDPE file and a regular BED/GFF/VCF file (Also supports BAM format as input and output).
PairToPair – Returns overlaps between two BEDPE files.
BamToBed – Converts BAM alignments to BED and BEDPE formats (Also supports BAM format as input and output).
BedToBam – Converts BED/GFF/VCF features (both blocked and unblocked) to BAM format.
BedToIgv - Creates a batch script to create IGV images at each interval defined in a BED/GFF/ VCF file.
Bed12ToBed6 – Splits BED12 features into discrete BED6 features.
SubtractBed - Removes the portion of an interval that is overlapped by another feature.
MergeBed – Merges overlapping features into a single feature.
FastaFromBed- Creates FASTA sequences from BED/GFF intervals.
MaskFastaFromBed – Masks a FASTA file based upon BED/GFF coordinates.
ShuffleBed – Permutes the locations of features within a genome.
SlopBed- Adjusts features by a requested number of base pairs.
SortBed – Sorts BED/GFF files in useful ways.
LinksBed – Creates an HTML links from a BED/GFF file.
ComplementBed - Returns intervals not spanned by features in a BED/GFF file.
Overlap – Computes the amount of overlap (positive values) or distance (negative values) between genome features and reports the result at the end of the same line.
GroupBy- Summarizes a dataset column based upon common column groupings. Akin to the SQL “group by” command.
BedTools homepage: http://code.google.com/p/bedtools/
Reference:
Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
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- •Quinlan AR and Hall IM 2010 BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 6 pp 841–842
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