convert2bed - manual page for convert2bed 2.4.39+dfsg1
convert2bed
- version:
- 2.4.39
- author:
- Alex Reynolds
- Usage:
- $ convert2bed --input=fmt [--output=fmt] [options] <
input > output
- Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF and WIG
genomic formats to BED or BEDOPS Starch (compressed BED)
- Input can be a regular file or standard input piped in using the hyphen
character ('-'):
- $ some_upstream_process ... | convert2bed --input=fmt -
> output
- Input (required):
--input=[bam|gff|gtf|gvf|psl|rmsk|sam|vcf|wig]
(-i <fmt>)
- Genomic format of input file (required)
- Output:
--output=[bed|starch] (-o <fmt>)
- Format of output file, either BED or BEDOPS Starch (optional, default is
BED)
- Other processing options:
--do-not-sort (-d)
- Do not sort BED output with sort-bed (not compatible with
--output=starch)
--max-mem=<value> (-m <val>)
- Sets aside <value> memory for sorting BED output. For example,
<value> can be 8G, 8000M or 8000000000 to specify 8 GB of memory
(default is 2G)
--sort-tmpdir=<dir> (-r <dir>)
- Optionally sets [dir] as temporary directory for sort data, when used in
conjunction with --max-mem=[value], instead of the host's
operating system default temporary directory
--starch-bzip2 (-z)
- Used with --output=starch, the compressed output explicitly
applies the bzip2 algorithm to compress intermediate data (default is
bzip2)
--starch-gzip (-g)
- Used with --output=starch, the compressed output applies
gzip compression on intermediate data
--starch-note="xyz..." (-e
"xyz...")
- Used with --output=starch, this adds a note to the Starch
archive metadata
--help |
--help[-bam|-gff|-gtf|-gvf|-psl|-rmsk|-sam|-vcf|-wig] (-h |
-h <fmt>)
- Show general help message (or detailed help for a specified input
format)
--version (-w)
- Show application version
The full documentation for convert2bed is maintained as a
Texinfo manual. If the info and convert2bed programs are
properly installed at your site, the command
- info convert2bed
should give you access to the complete manual.