6.3.3.1. convert2bed

The convert2bed binary converts common binary and text genomic formats (BAM, GFF, GTF, GVF, PSL, RepeatMasker annotation output (OUT), SAM, VCF and WIG) to unsorted or sorted, extended BED or BEDOPS Starch (compressed BED) with additional per-format options.

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

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-based computational cluster or local GNU Parallel installation.

6.3.3.1.1. Dependencies

Conversion of BAM and SAM input is dependent upon the installation of SAMtools and convert2bed. All *2starch wrapper scripts are further dependent on the installation of the starch binary, part of a typical BEDOPS installation.

6.3.3.1.2. Source

The convert2bed conversion tool is part of the binary and source downloads of BEDOPS. See the Installation documentation for more details.

6.3.3.1.3. 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

Tip

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.

6.3.3.1.4. Example

Please review documentation for each wrapper script to see format-specific examples of their use.