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

  • 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 matc

  • 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 fea

  • 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 “exclu

  • 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

  • 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 snaps

  • 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 over

  • 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 geno

  • 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

  • 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="

  • 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 s

  • 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 th

  • 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 “gro

  • bedtools jaccard

    Whereas the bedtools intersect tool enumerates each an every intersection between two sets of genomic intervals, one often needs a single statistic re

  • 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 wa

  • 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, ind

  • 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 int

  • 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, close

  • 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 inte

  • 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 occur

  • 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

  • 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 exa

  • 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 cove

  • 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 a

  • bedtools genomecov

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

  • 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, ind

  • bedtools multicov

    bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifica

  • 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 anothe

  • 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.