NAME
convert2bed - manual page for convert2bed 2.4.41+dfsg
DESCRIPTION
convert2bed
- version:
-
2.4.41
- 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
SEE ALSO
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.