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.