| Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations. |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bedtools
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| apply a function to a column for each overlapping interval | 2.27.1.2 | 16.01 | |
| use intervals to mask sequences from a FASTA file | 2.27.1 | 16.01 | |
| remove intervals based on overlaps | 2.27.1 | 16.01 | |
| use intervals to extract sequences from a FASTA file | 2.27.1 | 16.01 | |
| annotate coverage of features from multiple files | 2.27.1+galaxy1 | 16.01 | |
| reports the distances between features | 2.27.1 | 16.01 | |
| cluster overlapping/nearby intervals | 2.27.1 | 16.01 | |
| order the intervals | 2.27.1 | 16.01 | |
| Extract intervals not represented by an interval file | 2.27.1 | 16.01 | |
| generate random intervals in a genome | 2.27.1 | 16.01 | |
| computes the amount of overlap from two intervals | 2.27.1 | 16.01 | |
| create batch script for taking IGV screenshots | 2.27.1 | 16.01 | |
| adjust the size of intervals | 2.27.1 | 16.01 | |
| profile the nucleotide content of intervals in a FASTA file | 2.27.1 | 16.01 | |
| converter | 2.27.1 | 16.01 | |
| combines coverage intervals from multiple BEDGRAPH files | 2.27.1 | 16.01 | |
| create a HTML page of links to UCSC locations | 2.27.1 | 16.01 | |
| find overlapping intervals in various ways | 2.27.1+galaxy1 | 16.01 | |
| compute the coverage over an entire genome | 2.27.1 | 16.01 | |
| find overlapping intervals within a window around an interval | 2.27.1 | 16.01 | |
| calculate the distribution of relative distances | 2.27.1 | 16.01 | |
| converter | 2.27.1 | 16.01 | |
| make interval windows across a genome | 2.27.1 | 16.01 | |
| counts coverage from multiple BAMs at specific intervals | 2.27.1 | 16.01 | |
| of features in file B on the features in file A (bedtools coverage) | 2.27.1+galaxy1 | 16.01 | |
| group by common cols and summarize other cols | 2.27.1 | 16.01 | |
| calculate Fisher statistic between two feature files | 2.27.1+galaxy1 | 16.01 | |
| calculate the distribution of relative distances between two files | 2.27.1+galaxy1 | 16.01 | |
| 2.27.1 | 16.01 | ||
| create new intervals from the flanks of existing intervals | 2.27.1 | 16.01 | |
| converter | 2.27.1 | 16.01 | |
| randomly redistrubute intervals in a genome | 2.27.1 | 16.01 | |
| tag BAM alignments based on overlaps with interval files | 2.27.1+galaxy1 | 16.01 | |
| replicate lines based on lists of values in columns | 2.27.1 | 16.01 | |
| find the closest, potentially non-overlapping interval | 2.27.1 | 16.01 | |
| converter | 2.27.1 | 16.01 | |
| combine overlapping/nearby intervals into a single interval | 2.27.1 | 16.01 | |
| identifies common intervals among multiple interval files | 2.27.1+galaxy1 | 16.01 | |