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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>
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Function: For each feature in A, finds the closest feature (upstream or downstream) in B.
Usage: bedtools closest [OPTIONS] -a <FILE> -b <FILE1, FILE2, ..., FILEN>
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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>
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Function: Remove records from a bed file that are out of annotated chromosome ranges.
Usage: bedClip [options] input.bed chrom.sizes output.bed
Supported input format:
BED
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Function: Convert genomic coordinates from one assembly (e.g. hg19) to another (e.g. hg38)
Usage: liftOver oldFile map.chain newFile unMapped
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Function: Shift/extend each feature by requested number of base pairs.
Usage: bedtools shift [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-s or (-m and -p)]
Supported input format:
BED, GFF, GTF, VCF
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Function: Extend length of entries in bed 6+ data to be at least the given length, taking strand directionality into account.
Usage: bedExtendRanges database length files(s)
Supported input format:
BED
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Function: Calculate the relative distance distribution between two feature files.
Usage: bedtools reldist [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
Supported input format:
BED, GFF, GTF, VCF
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Function: bedtools bamtofastq is a conversion utility for extracting FASTQ records
from sequence alignments in BAM format.
Usage: bamToFastq [OPTIONS] -i -fq
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Function: Clusters overlapping/nearby BED/GFF/VCF intervals
Usage: clusterBed [OPTIONS] -i <BED/GFF/VCF>
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Function: Generate a random set of intervals in BED6 format, the number and the size of the intervals can be defined by the user.
Usage: bedtools random [OPTIONS] -g <GENOME>
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Function: Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files.
Usage: annotateBed [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
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Function: Randomly permute the genomic locations of a feature file among a genome defined in a genome file.
Usage: shuffleBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
Supported input format:
BED, GFF, GTF, VCF
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Function: 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.
Usage: bedtools multicov [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>
Supported input format:
BED, BAM, GFF, GTF, VCF
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Function: Calculate Jaccard statistic between two feature files. Jaccard is the length of the intersection over the union. Values range from 0 (no intersection) to 1 (self intersection).
Usage: bedtools jaccard [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>