bedtools

Version:
2.29.x
Identifier: TL_43392c.c8
Tool

Description


BEDTools is an extensive suite of utilities for comparing genomic features in BED format.

Subtools

  • bedtools cluster

    Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined.

  • bedtools maskfasta

    bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.

  • bedtools map

    bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features. For example, one could use bedtools map to compute the average score of BEDGRAPH records that overlap genes.

  • bedtools shuffle

    bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the s

  • bedtools nuc

    Profiles the nucleotide content of intervals in a fasta file

  • bedtools slop

    bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size).

  • bedtools igv

    bedToIgv creates an IGV (http://www.broadinstitute.org/igv/) batch script (see http:// www.broadinstitute.org/igv/batch for details) such that a snapshot will be taken at each features in a feature file.

  • bedtools substract

    bedtools subtract bedtools` subtract searches for features in B that overlap A by at least the number of base pairs given by the -f option. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported. If a feature in B does not overlap a feature in

  • bedtools unionbedg

    bedtools unionbedg combines multiple BEDGRAPH files into a single file such that one can directly compare coverage (and other text-values such as genotypes) across multiple sample

  • bedtools window

    Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.

  • bedtools complement

    bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.

  • bedtools shift

    bedtools shift will move each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2+<shift>,$3+<shift>}', bedtools shift will restrict the resizing to the size of the chromosome (i.e. no features before 0 or past the chromosome end).

  • bedtools random

    bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.

  • bedtools annotate

    bedtools annotate, well, 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 with a single command.

  • bedtools groupby

    bedtools groupby is a useful tool that mimics the “group by” clause in database systems. Given a file or stream that is sorted by the appropriate “grouping columns” (-g), groupby will compute summary statistics on another column (-c) in the file or stream. This will work with output from all BEDTools as well as any other tab-delimited file or stream. As such, this is a generally useful tool for al

  • bedtools jaccard

    Whereas the bedtools intersect tool enumerates each an every intersection between two sets of genomic intervals, one often needs a single statistic reflecting the similarity of the two sets based on the intersections between them. The Jaccard statistic is used in set theory to represent the ratio of the intersection of two sets to the union of the two sets. Similarly, Favorov et al [1] reported th

  • bedtools links

    Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.

  • bedtools bedpetobam

    bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.

  • bedtools makewindows

    Make interval windows across a genome.

  • bedtools multiinter

    Identifies common intervals among multiple interval files.

  • bedtools sort

    The bedtools sort tool sorts a feature file by chromosome and other criteria.

  • bedtools reldist

    Traditional approaches to summarizing the similarity between two sets of genomic intervals are based upon the number or proportion of intersecting intervals. However, such measures are largely blind to spatial correlations between the two sets where, despite consistent spacing or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap, yet they are mu

  • bedtools coveragebed

    coverageBed computes both the depth and breadth of coverage of features in file A across the features in file B

  • bedtools closest

    Similar to intersect, closest searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closest will report the nearest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closest will report an overlapping featu

  • bedtools bamtofastq

    bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.

  • bedtools flank

    bedtools flank will create two new flanking intervals for each interval in a BED/GFF/VCF file. Note that flank will restrict the created flanking intervals to the size of the chromosome (i.e. no start < 0 and no end > chromosome size).

  • bedtools overlap

    overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools.

  • bedtools pairtopair

    pairToPair compares two BEDPE files in search of overlaps where each end of a BEDPE feature in A overlaps with the ends of a feature in B. For example, using pairToPair, one could screen for the exact same discordant paired-end alignment in two files. This could suggest (among other things) that the discordant pair suggests the same structural variation in each file/sample.

  • bedtools bamtobed

    bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.

  • bedtools bed12tobed6

    bed12ToBed6 is a convenience tool that converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features. For example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).

  • bedtools coverage

    The bedtools coverage tool computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. One advantage that bedtools coverage offers is that it not only counts the number of features that overlap an in

  • bedtools fisher

    Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files. Traditionally, in order to test whether 2 sets of intervals are related spatially, we resort to shuffling the genome and checking the simulated (shuffled) versus the observed. We can do the same analytically for many scenarios using Fisher’s Exact Test. This implementation can calculate the number of overlaps

  • bedtools genomecov

    bedtools genomecov computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.

  • bedtools expand

    expand window

  • bedtools bedtobam

    bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.

  • bedtools multicov

    bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.

  • bedtools intersect

    By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with

  • bedtools genomecov_bed2bedgraph

    bed to bedgraph converter (bedgraph used for tracks)

  • bedtools merge

    bedtools merge combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.

  • bedtools getfasta

    bedtools getfasta extracts sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.