convert2bed tool 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.
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
We also provide
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.
The following compiles
convert2bed and copies the binary and wrappers to
$ make && make install
Generally, to convert data in format
xyz to sorted BED:
$ convert2bed -i xyz < input.xyz > output.bed
-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-gff etc. with
convert2bed to get a format-specific description of the conversion procedure and options.
This tool is dependent upon
samtools to handle BAM conversion, and BEDOPS
starch 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.
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.