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Function: 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).
Usage: flankBed [OPTIONS] -i -g [-b or (-l and -r)]
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Function: Analyse coverage by bed files - chromosome bychromosome and genome-wide
Usage: bedCoverage genomeDatabase bedFile
Supported input format:
BED
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Function: bedtools merge combines overlapping or “book-ended†features in an interval
file into a single feature which spans all of the combined features.
Usage: mergeBed [OPTIONS] -i
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Function: 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.
Usage: multiBamCov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed
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Function: bedtools complement returns all intervals in a genome that are not
covered by at least one interval in the input BED/GFF/VCF file.
Usage: complementBed -i <BED/GFF/VCF> -g <GENOME>
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Function: Extract item of given name from bigBed
Usage: bigBedNamedItems file.bb name output.bed
Supported input format:
bigBed
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Function: 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 “overlapâ€
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 both BED/GFF/VCF and BAM files as input.
Usage: intersectBed [OPTIONS] -a \
-b
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Function: 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 feature as the closest—that is, it does not restrict to closest non-overlapping feature. The following iconic “cheatsheet†summarizes the funcitonality available through the various optyions provided by the closest tool.
Usage: closestBed [OPTIONS] -a -b
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Function: 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-,$3+}',
bedtools slop will restrict the resizing to the size of the chromosome
(i.e. no start < 0 and no end > chromosome size).
Usage: slopBed [OPTIONS] -i -g [-b or (-l and -r)]
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Function: bedtools subtract searches for features in B that overlap A. 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.
Usage: subtractBed [OPTIONS] -a -b
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Function: Map features in a B file onto features in an A file and apply statistics and/or summary operations on those features
Usage: bedtools map [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
Supported input format:
BED, GFF, GTF, VCF
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Function: Create a bed file (just bed3) that contains the regions common to all inputs.
Usage: bedCommonRegions file1 file2 file3 ... fileN
Supported input format:
BED
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Function: Perform Fisher's test to see if the amount of overlap between the two sets of intervals is more or less than expected, given their coverage and the genome size.
Usage: bedtools fisher [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam> -g <genome file>
Supported input format:
BED, BAM, GFF, GTF, VCF
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Function: Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.
Usage: bedtools igv [OPTIONS] -i <bed/gff/vcf>
Supported input format:
BED, GFF, GTF, VCF
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Function: Summarize a dataset column based upon common column groupings. Akin to the SQL "group by" command.
Usage: bedtools groupby [OPTIONS] -i <input> -g <group columns> -c <op. column> -o <operation>
Supported input format:
BED