| bedtools shuffle |
bedtools shuffle [OPTIONS] -i -g
|
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 significance of associations
of one feature with another. |
| bedtools bamtobed |
bedtools bamtobed [OPTIONS] -i <BAM> |
Convert sequence alignments in BAM format into BED, BED12, and/or BEDPE records |
| bedtools intersect |
bedtools intersect [OPTIONS] -a <FILE> -b <FILE1, FILE2, ..., FILEN>
|
Screen for overlaps between two sets of genomic features with fine control as to how the intersections are reported. |
| bedtools bamtofastq |
bedtools bamtofastq [OPTIONS] -i -fq
|
bedtools bamtofastq is a conversion utility for extracting FASTQ records
from sequence alignments in BAM format. |
| bedtools flank |
bedtools flank [OPTIONS] -i -g [-b or (-l and -r)]
|
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 cluster |
bedtools cluster [OPTIONS] -i
|
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 slop |
bedtools slop [OPTIONS] -i -g [-b or (-l and -r)]
|
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). |
| bedtools coverage |
bedtools coverage [OPTIONS] -a \
-b
|
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 interval in file A, it also
computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus,
bedtools coverage also computes the breadth of coverage observed for each interval in A. |
| bedtools subtract |
bedtools subtract [OPTIONS] -a -b
|
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. |
| genomeCoverageBed |
genomeCoverageBed [OPTIONS] [-i|-ibam] -g (iff. -i)
|
bedtools genomecov computes histograms (default), per-base reports (-d)
and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences)
for a given genome. |
| bamToBed |
bamToBed [OPTIONS] -i |
bedtools bamtobed is a conversion utility that converts sequence alignments
in BAM format into BED, BED12, and/or BEDPE records. |
| bedtools annotate |
bedtools annotate [OPTIONS] -i -files FILE1 FILE2 FILE3 ... FILEn
|
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 complement |
bedtools complement -i -g
|
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 [OPTIONS] -i -g [-s or (-m and -p)]
|
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+,$3+}',
bedtools shift will restrict the resizing to the size of the chromosome
(i.e. no features before 0 or past the chromosome end). |
| coverageBed |
coverageBed [OPTIONS] -a \
-b
|
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 interval in file A, it also
computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus,
bedtools coverage also computes the breadth of coverage observed for each interval in A. |
| bedtools genomecov |
bedtools genomecov [OPTIONS] [-i|-ibam] -g (iff. -i)
|
bedtools genomecov computes histograms (default), per-base reports (-d)
and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences)
for a given genome. |
| bamToFastq |
bamToFastq [OPTIONS] -i -fq |
bedtools bamtofastq is a conversion utility for extracting FASTQ records
from sequence alignments in BAM format. |
| bedtools map |
bedtools map -a genes.bed -b peaks.bedgraph -c 4 -o mean
|
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. |
| bedtools reldist |
bedtools reldist [OPTIONS] -a -b
|
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, dpesite consistent spacing
or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap,
yet they are much closer to one another than two sets of random intervals). Favorov et al [1] proposed
a relative distance metric that describes distribution of relative distances between each interval in
one set nd the two closest intervals in another set (see figure above). If there is no spatial
correlation between the two sets, one would expect the relative distances to be uniformaly distributed
among the relative distances ranging from 0 to 0.5. If, however, the intervals tend to be much closer than expected
by chance, the distribution of observed relative distances would be shifted towards low relative distance values (e.g., the figure below). |
| clusterBed |
clusterBed [OPTIONS] -i
|
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. |