Man page - convert2bed(1)
Packages contains this manual
- starchcluster_sge(1)
- bedmap(1)
- bedops-starch(1)
- bam2bed(1)
- starchstrip(1)
- bam2bed_slurm(1)
- gff2bed(1)
- bam2starch_slurm(1)
- gtf2starch(1)
- bam2starch_sge(1)
- psl2bed(1)
- psl2starch(1)
- vcf2starch(1)
- closest-features(1)
- bedops(1)
- bedextract(1)
- gtf2bed(1)
- sort-bed(1)
- wig2bed(1)
- bam2bed_sge(1)
- sam2starch(1)
- gvf2bed(1)
- gvf2starch(1)
- sam2bed(1)
- rmsk2starch(1)
- bam2starch(1)
- unstarch(1)
- gff2starch(1)
- starchcluster_slurm(1)
- starchcat(1)
- rmsk2bed(1)
- convert2bed(1)
- vcf2bed(1)
- wig2starch(1)
apt-get install bedops
Manual
CONVERT2BED
NAMEDESCRIPTION
SEE ALSO
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.