.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH CONVERT2BED "1" "October 2018" "convert2bed 2.4.35+dfsg" "User Commands"
.SH NAME
convert2bed \- manual page for convert2bed 2.4.35+dfsg
.SH DESCRIPTION
convert2bed
.TP
version:
2.4.35
.TP
author:
Alex Reynolds
.IP
Usage:
.IP
\f(CW$ convert2bed --input=fmt [--output=fmt] [options] < input > output\fR
.IP
Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF
and WIG genomic formats to BED or BEDOPS Starch (compressed BED)
.IP
Input can be a regular file or standard input piped in using the
hyphen character ('\-'):
.IP
\f(CW$ some_upstream_process ... | convert2bed --input=fmt - > output\fR
.IP
Input (required):
.HP
\fB\-\-input\fR=\fI\,[bam\/\fR|gff|gtf|gvf|psl|rmsk|sam|vcf|wig] (\fB\-i\fR <fmt>)
.IP
Genomic format of input file (required)
.IP
Output:
.HP
\fB\-\-output\fR=\fI\,[bed\/\fR|starch] (\fB\-o\fR <fmt>)
.IP
Format of output file, either BED or BEDOPS Starch (optional, default is BED)
.IP
Other processing options:
.HP
\fB\-\-do\-not\-sort\fR (\fB\-d\fR)
.IP
Do not sort BED output with sort\-bed (not compatible with \fB\-\-output\fR=\fI\,starch\/\fR)
.HP
\fB\-\-max\-mem=\fR<value> (\fB\-m\fR <val>)
.IP
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)
.HP
\fB\-\-sort\-tmpdir=\fR<dir> (\fB\-r\fR <dir>)
.IP
Optionally sets [dir] as temporary directory for sort data, when used in
conjunction with \fB\-\-max\-mem\fR=\fI\,[value]\/\fR, instead of the host's operating system
default temporary directory
.HP
\fB\-\-starch\-bzip2\fR (\fB\-z\fR)
.IP
Used with \fB\-\-output\fR=\fI\,starch\/\fR, the compressed output explicitly applies the bzip2
algorithm to compress intermediate data (default is bzip2)
.HP
\fB\-\-starch\-gzip\fR (\fB\-g\fR)
.IP
Used with \fB\-\-output\fR=\fI\,starch\/\fR, the compressed output applies gzip compression on
intermediate data
.HP
\fB\-\-starch\-note=\fR"xyz..." (\fB\-e\fR "xyz...")
.IP
Used with \fB\-\-output\fR=\fI\,starch\/\fR, this adds a note to the Starch archive metadata
.HP
\fB\-\-help\fR | \fB\-\-help[\-bam\fR|\-gff|\-gtf|\-gvf|\-psl|\-rmsk|\-sam|\-vcf|\-wig] (\fB\-h\fR | \fB\-h\fR <fmt>)
.IP
Show general help message (or detailed help for a specified input format)
.HP
\fB\-\-version\fR (\fB\-w\fR)
.IP
Show application version
.SH "SEE ALSO"
The full documentation for
.B convert2bed
is maintained as a Texinfo manual.  If the
.B info
and
.B convert2bed
programs are properly installed at your site, the command
.IP
.B info convert2bed
.PP
should give you access to the complete manual.