Addition of a pairedBamToBed12 utility by Nicolas Bertin (OSC RIKEN Yokohama) to BEDTools Created by Aaron Quinlan Spring 2009.
Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved. Released under GNU public license version 2 (GPL v2).
Repository: https://github.com/nicolas-bertin/bedtools-pairedBamToBed12
BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats. In this branch is added pairedBamToBed12 which converts a name sorted paired-end sequences bam file into a 2-block bed12 formatted file.
See the extensive PDF manual included at: http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf.
This manual covers many common usage examples. There are also examples available at: http://code.google.com/p/bedtools/wiki/Usage http://code.google.com/p/bedtools/wiki/UsageAdvanced Note that the manual does not reflect the pairedBamToBed12 addition.
- Unpack the source downloaded tarball.
- cd into the expanded folder.
- Type "make clean" and hit enter.
- Type "make all" and hit enter.
- If you encountered no errors, then all of the BED Tools should now be in bin/ If not, try to troubleshoot then email me: aaronquinlan at gmail dot com
- Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin.
- Use the tools.
| Utility | Description |
|---|---|
| intersectBed (BAM) | Returns overlaps between two BED/GFF/VCF files. |
| pairToBed (BAM) | Returns overlaps between a paired-end BED file and a regular BED/VCF/GFF file. |
| bamToBed (BAM) | Converts BAM alignments to BED6, BED12, or BEDPE format. |
| bedToBam (BAM) | Converts BED/GFF/VCF features to BAM format. |
| bed12ToBed6 | Converts "blocked" BED12 features to discrete BED6 features. |
| bedToIgv | Creates IGV batch scripts for taking multiple snapshots from BED/GFF/VCF features. |
| coverageBed (BAM) | Summarizes the depth and breadth of coverage of features in one BED versus features (e.g, "windows", exons, etc.) defined in another BED/GFF/VCF file. |
| genomeCoverageBed (BAM) | Creates either a histogram, BEDGRAPH, or a "per base" report of genome coverage. |
| unionBedGraphs | Combines multiple BedGraph files into a single file, allowing coverage/other comparisons between them. |
| annotateBed | Annotates one BED/VCF/GFF file with overlaps from many others. |
| groupBy | Summarizes data in a file/stream based on common columns. |
| overlap | Returns the number of bases pairs of overlap b/w two features on the same line. |
| *pairToPair * | Returns overlaps between two paired-end BED files. |
| closestBed | Returns the closest feature to each entry in a BED/GFF/VCF file. |
| subtractBed | Removes the portion of an interval that is overlapped by another feature. |
| windowBed (BAM) | Returns overlaps between two BED/VCF/GFF files based on a user-defined window. |
| mergeBed | Merges overlapping features into a single feature. |
| complementBed | Returns all intervals _not_ spanned by the features in a BED/GFF/VCF file. |
| fastaFromBed | Creates FASTA sequences based on intervals in a BED/GFF/VCF file. |
| maskFastaFromBed | Masks a FASTA file based on BED coordinates. |
| shuffleBed | Randomly permutes the locations of a BED file among a genome. |
| slopBed | Adjusts each BED entry by a requested number of base pairs. |
| sortBed | Sorts a BED file by chrom, then start position. Other ways as well. |
| linksBed | Creates an HTML file of links to the UCSC or a custom browser. |
| pairedBamToBed12 | Convert a name sorted paired-end sequences bam file into a 2-block bed12 formatted file. |