Bedtools
Manipulate tabular genomic files.
: BEDOps
The BEDTools [1] utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together.
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.
The fact that all of the BEDTools accept input from “standard input (stdin)” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. Most recently, I have added support for sequence alignments in BAM (http://samtools.sourceforge.net/) format, as well as for features in VCF and GFF, as well as “blocked” BED format. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets.
You can obtain bedtools as a zipped source folder or by using GIT (better) from the following repository https://github.com/arq5x/bedtools2.git [2].
A picture-rich operation manual is hosted at http://bedtools.readthedocs.org/en/latest [3].
Python Afficionados, can download a python version of BEDTools used in Galaxy
$ bedtools
bedtools: flexible tools for genome arithmetic and DNA sequence analysis.
usage: bedtools <subcommand> [options]
The bedtools sub-commands include:
[ Genome arithmetic ]
intersect Find overlapping intervals in various ways.
window Find overlapping intervals within a window around an interval.
closest Find the closest, potentially non-overlapping interval.
coverage Compute the coverage over defined intervals.
map Apply a function to a column for each overlapping interval.
genomecov Compute the coverage over an entire genome.
merge Combine overlapping/nearby intervals into a single interval.
cluster Cluster (but don't merge) overlapping/nearby intervals.
complement Extract intervals _not_ represented by an interval file.
subtract Remove intervals based on overlaps b/w two files.
slop Adjust the size of intervals.
flank Create new intervals from the flanks of existing intervals.
sort Order the intervals in a file.
random Generate random intervals in a genome.
shuffle Randomly redistrubute intervals in a genome.
sample Sample random records from file using reservoir sampling.
annotate Annotate coverage of features from multiple files.
[ Multi-way file comparisons ]
multiinter Identifies common intervals among multiple interval files.
unionbedg Combines coverage intervals from multiple BEDGRAPH files.
[ Paired-end manipulation ]
pairtobed Find pairs that overlap intervals in various ways.
pairtopair Find pairs that overlap other pairs in various ways.
[ Format conversion ]
bamtobed Convert BAM alignments to BED (& other) formats.
bedtobam Convert intervals to BAM records.
bamtofastq Convert BAM records to FASTQ records.
bedpetobam Convert BEDPE intervals to BAM records.
bed12tobed6 Breaks BED12 intervals into discrete BED6 intervals.
[ Fasta manipulation ]
getfasta Use intervals to extract sequences from a FASTA file.
maskfasta Use intervals to mask sequences from a FASTA file.
nuc Profile the nucleotide content of intervals in a FASTA file.
[ BAM focused tools ]
multicov Counts coverage from multiple BAMs at specific intervals.
tag Tag BAM alignments based on overlaps with interval files.
[ Statistical relationships ]
jaccard Calculate the Jaccard statistic b/w two sets of intervals.
reldist Calculate the distribution of relative distances b/w two files.
[ Miscellaneous tools ]
overlap Computes the amount of overlap from two intervals.
igv Create an IGV snapshot batch script.
links Create a HTML page of links to UCSC locations.
makewindows Make interval "windows" across a genome.
groupby Group by common cols. & summarize oth. cols. (~ SQL "groupBy")
expand Replicate lines based on lists of values in columns.
[ General help ]
--help Print this help menu.
--version What version of bedtools are you using?.
--contact Feature requests, bugs, mailing lists, etc.
References:
- ↑
Aaron R Quinlan, Ira M Hall
BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics: 2010, 26(6);841-2
[PubMed:20110278] ##WORLDCAT## [DOI] (I p) - ↑ https://github.com/arq5x/bedtools2.git
- ↑ http://bedtools.readthedocs.org/en/latest
