| bedtools shuffle |
bedtools shuffle [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> |
Randomly permute the genomic locations of a feature file among a genome defined in a genome file. |
| 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. |
| bedRemoveOverlap |
bedRemoveOverlap in.bed out.bed |
Remove overlapping records from a (sorted) bed file. |
| bedtools bamtofastq |
bedtools bamtofastq [OPTIONS] -i <BAM> -fq <FASTQ> |
Extract FASTQ records from sequence alignments in BAM format. |
| bedtools flank |
bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)] |
Creates flanking interval(s) for each BED/GFF/VCF feature |
| bedtools cluster |
bedtools cluster [OPTIONS] -i <BED/GFF/VCF> |
Clusters overlapping/nearby BED/GFF/VCF intervals |
| bedtools coverage |
bedtools coverage [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf> |
Returns the depth and breadth of coverage of features from B on the intervals in A. |
| bedtools slop |
bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-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 annotate |
bedtools annotate [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn |
Annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. |
| bedtools complement |
bedtools complement -i <BED/GFF/VCF> -g <GENOME> |
Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. |
| genomeCoverageBed |
genomeCoverageBed [OPTIONS] [-i|-ibam] -g (iff. -i)
|
Computes histograms or per-base reports of feature coverage (e.g., aligned sequences) for a given genome. |
| bedtools subtract |
bedtools subtract [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF> |
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. |
| bedtools shift |
bedtools shift [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-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). |
| bedtools genomecov |
bedtools genomecov [OPTIONS] [-i|-ibam] <bed/gff/vcf> -g <genome> |
Computes histograms or per-base reports of feature coverage (e.g., aligned sequences) for a given genome. |
| coverageBed |
coverageBed [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
|
Returns the depth and breadth of coverage of features from B on the intervals in A. |
| clusterBed |
clusterBed [OPTIONS] -i <BED/GFF/VCF>
|
Clusters overlapping/nearby BED/GFF/VCF intervals |
| bedtools reldist |
bedtools reldist [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF> |
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). |
| bamToFastq |
bamToFastq [OPTIONS] -i -fq |
bedtools bamtofastq is a conversion utility for extracting FASTQ records
from sequence alignments in BAM format. |
| bedtools merge |
bedtools merge [OPTIONS] -i <BED/GFF/VCF/BAM> |
Merges overlapping BED/GFF/VCF entries into a single interval. |
| bedtools closest |
bedtools closest [OPTIONS] -a <FILE> -b <FILE1, FILE2, ..., FILEN> |
For each feature in A, finds the closest feature (upstream or downstream) in B. |