.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BAM2STARCH_SGE "1" "February 2017" "bam2starch_sge 2.4.20+dfsg" "User Commands"
.SH NAME
bam2starch_sge \- manual page for bam2starch_sge 2.4.20+dfsg
.SH SYNOPSIS
.B bam2starch_sge
[\fI\,--help\/\fR] [\fI\,--clean\/\fR] \fI\,<input-indexed-bam-file> \/\fR[\fI\,output-starch-file\/\fR]
.SH DESCRIPTION
.IP
Pass in the name of an indexed BAM file to create a Starch archive using the cluster.
.IP
(stdin isn't supported through this wrapper script, but Starch supports it natively.)
.IP
Add \fB\-\-clean\fR to remove <input\-indexed\-bam\-file> after starching it up.
.IP
You can pass in the name of the output Starch archive to be created.
Otherwise, the output will have the same name as the input file, with an additional
.TP
\&'.starch' ending.
If the input file ends with '.bam', that will be stripped off.
.SH "SEE ALSO"
The full documentation for
.B bam2starch_sge
is maintained as a Texinfo manual.  If the
.B info
and
.B bam2starch_sge
programs are properly installed at your site, the command
.IP
.B info bam2starch_sge
.PP
should give you access to the complete manual.