https://github.com/alexpreynolds/convert2bed

Convert common binary and text genomic formats to BED
https://github.com/alexpreynolds/convert2bed

bam bed c conversion

Last synced: about 1 month ago
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Convert common binary and text genomic formats to BED

• Host: GitHub
• URL: https://github.com/alexpreynolds/convert2bed
• Owner: alexpreynolds
• License: gpl-2.0
• Created: 2014-11-07T22:11:09.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2020-08-25T01:17:38.000Z (almost 5 years ago)
• Last Synced: 2025-02-17T16:38:49.706Z (4 months ago)
• Topics: bam, bed, c, conversion
• Language: C
• Homepage: http://alexpreynolds.github.io/convert2bed/
• Size: 192 KB
• Stars: 2
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
convert2bed

===========

Note! Hey! Read this! This is really important!

-----------------------------------------------

Hi! At this time, all active development on `convert2bed` is being done within [BEDOPS](https://github.com/bedops/bedops). If you want the latest features and bug fixes in `convert2bed` (and there have been many since 2015!), I very strongly suggest you fork or review the code in BEDOPS.

[![Build Status](https://travis-ci.org/alexpreynolds/convert2bed.svg?branch=master)](https://travis-ci.org/alexpreynolds/convert2bed)

Stop reading and go download BEDOPS! This code is dead!

-------------------------------------------------------

The `convert2bed` tool converts common binary and text genomic formats ([BAM](http://samtools.github.io/hts-specs/SAMv1.pdf), [GFF](http://www.sequenceontology.org/gff3.shtml), [GTF](http://mblab.wustl.edu/GTF22.html), [GVF](http://www.sequenceontology.org/resources/gvf.html#summary), [PSL](http://genome.ucsc.edu/FAQ/FAQformat.html#format2), [RepeatMasker annotation output](http://www.repeatmasker.org/webrepeatmaskerhelp.html), [SAM](http://samtools.github.io/hts-specs/SAMv1.pdf), [VCF](http://samtools.github.io/hts-specs/VCFv4.2.pdf) and [WIG](http://genome.ucsc.edu/goldenpath/help/wiggle.html)) to unsorted or [sorted, extended BED](http://bedops.readthedocs.org/en/latest/content/reference/file-management/sorting/sort-bed.html) or [BEDOPS Starch](http://bedops.readthedocs.org/en/latest/content/reference/file-management/compression/starch.html) (compressed BED) with additional per-format options. 

Convenience wrapper `bash` scripts are provided for each format that convert standard input to unsorted or sorted BED, or to BEDOPS Starch (compressed BED). Scripts expose format-specific ``convert2bed`` options. 

Why are you still reading this?! Please use BEDOPS!

---------------------------------------------------

We also provide ``bam2bed_sge``, ``bam2bed_gnuParallel``, ``bam2starch_sge`` and ``bam2starch_gnuParallel`` convenience scripts, which parallelize the conversion of indexed BAM to BED or to BEDOPS Starch via a [Sun Grid Engine](http://en.wikipedia.org/wiki/Oracle_Grid_Engine)-based computational cluster or local [GNU Parallel](http://en.wikipedia.org/wiki/GNU_parallel) installation.

Installation

------------

The following compiles `convert2bed` and copies the binary and wrappers to `/usr/local/bin`:

    $ make && make install

Usage

-----

Generally, to convert data in format `xyz` to sorted BED:

    $ convert2bed -i xyz < input.xyz > output.bed

Add the `-o starch` option to write a BEDOPS Starch file, which stores compressed BED data and feature metadata:

    $ convert2bed -i xyz -o starch < input.xyz > output.starch

Wrappers are available for each of the supported formats to convert to BED or Starch, *e.g.*:

    $ bam2bed < reads.bam > reads.bed

    $ bam2starch < reads.bam > reads.starch

Format-specific options are available for each wrapper; use `--help` with a wrapper script or `--help-bam`, `--help-gff` etc. with `convert2bed` to get a format-specific description of the conversion procedure and options.

Dependencies

------------

This tool is dependent upon [`samtools`](https://github.com/samtools/samtools) to handle BAM conversion, and BEDOPS [`sort-bed`](http://bedops.readthedocs.org/en/latest/content/reference/file-management/sorting/sort-bed.html) and [`starch`](http://bedops.readthedocs.org/en/latest/content/reference/file-management/compression/starch.html) to generate sorted BED and Starch (compressed BED) output. The directory containing these binaries should be present in the end user's `PATH` environment variable. 

If the `samtools` binary is not present, BAM conversion will fail. If the `sort-bed` binary is not installed, all format conversions will fail with default sort rules applied. If the `starch` binary is not installed, the `starch` output format option will be unavailable.