Genomic Interval Manipulation

bedtools shuffle
Function: Randomly permute the genomic locations of a feature file among a genome defined in a genome file.
Usage: bedtools shuffle [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
Supported input format: BED, GFF, GTF, VCF
bedtools makewindows
Function: Makes adjacent or sliding windows across a genome or regions defined in a BED file.
Usage: bedtools makewindows [OPTIONS] [-g <genome> OR -b <bed>] [ -w <window_size> OR -n <number of windows> ]
Supported input format: BED
bedtools intersect
Function: Screen for overlaps between two sets of genomic features with fine control as to how the intersections are reported.
Usage: bedtools intersect [OPTIONS] -a <FILE> -b <FILE1, FILE2, ..., FILEN>
Supported input format: BED, BAM, GFF, GTF, VCF
bedtools slop
Function: Add requested base pairs of slop to each feature
Usage: bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
Supported input format: BED, GFF, GTF, VCF
bedtools coverage
Function: Returns the depth and breadth of coverage of features from B on the intervals in A.
Usage: bedtools coverage [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
Supported input format: BED, GFF, GTF, VCF
bedtools genomecov
Function: Computes histograms or per-base reports of feature coverage (e.g., aligned sequences) for a given genome.
Usage: bedtools genomecov [OPTIONS] [-i|-ibam] <bed/gff/vcf> -g <genome>
Supported input format: BED, BAM, GFF, GTF, VCF
bedtools flank
Function: Creates flanking interval(s) for each BED/GFF/VCF feature
Usage: bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
Supported input format: BED, GFF, GTF, VCF
bedtools annotate
Function: Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files.
Usage: bedtools annotate [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
Supported input format: BED, GFF, GTF, VCF
bedRemoveOverlap
Function: Remove overlapping records from a (sorted) bed file.
Usage: bedRemoveOverlap in.bed out.bed
Supported input format: BED
bedtools cluster
Function: Clusters overlapping/nearby BED/GFF/VCF intervals
Usage: bedtools cluster [OPTIONS] -i <BED/GFF/VCF>
Supported input format: BED, GFF, GTF, VCF
genomeCoverageBed
Function: Computes histograms or per-base reports of feature coverage (e.g., aligned sequences) for a given genome.
Usage: genomeCoverageBed [OPTIONS] -i <bed/gff/vcf> -g <genome>
Supported input format: BED, BAM, GFF, GTF, VCF
bedtools subtract
Function: Removes the portion(s) of intervals (in bed file A) that is overlapped by another feature(s) (defined in bed file B).
Usage: bedtools subtract [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
Supported input format: BED, GFF, GTF, VCF
bedtools complement
Function: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
Usage: bedtools complement -i <BED/GFF/VCF> -g <GENOME>
coverageBed
Function: Returns the depth and breadth of coverage of features from B on the intervals in A.
Usage: coverageBed [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
bigBedSummary
Function: Extract summary information from a bigBed file.
Usage: bigBedSummary file.bb chrom start end dataPoints
Supported input format: bigBed