Shayan Doust pushed to branch master at Debian Med / covtobed
Commits: 43ec387a by Shayan Doust at 2020-05-31T18:08:16+01:00 Manpages for covtobed - - - - - 2 changed files: - + debian/covtobed.manpages - + debian/mans/covtobed.1 Changes: ===================================== debian/covtobed.manpages ===================================== @@ -0,0 +1 @@ +debian/mans/covtobed.1 ===================================== debian/mans/covtobed.1 ===================================== @@ -0,0 +1,63 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8. +.TH COVTOBED "1" "May 2020" "covtobed 1.1.2" "User Commands" +.SH NAME +covtobed \- a tool to generate BED coverage tracks from BAM files +.SH SYNOPSIS +.B covtobed +[\fI\,options\/\fR] [\fI\,BAM\/\fR]... +.SH DESCRIPTION +Reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. +.SH OPTIONS +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-\-version\fR +show program's version number and exit +.TP +\fB\-\-physical\-coverage\fR +compute physical coverage (needs paired alignments in input) +.TP +\fB\-q\fR MINQ, \fB\-\-min\-mapq\fR=\fI\,MINQ\/\fR +skip alignments whose mapping quality is less than MINQ +(default: 0) +.TP +\fB\-m\fR MINCOV, \fB\-\-min\-cov\fR=\fI\,MINCOV\/\fR +print BED feature only if the coverage is bigger than +(or equal to) MINCOV (default: 0) +.TP +\fB\-x\fR MAXCOV, \fB\-\-max\-cov\fR=\fI\,MAXCOV\/\fR +print BED feature only if the coverage is lower than +MAXCOV (default: 100000) +.TP +\fB\-l\fR MINLEN, \fB\-\-min\-len\fR=\fI\,MINLEN\/\fR +print BED feature only if its length is bigger (or equal +to) than MINLELN (default: 1) +.TP +\fB\-d\fR, \fB\-\-discard\-invalid\-alignments\fR +skip duplicates, failed QC, and non primary alignment, +minq>0 (or user\-defined if higher) (default: 0) +.TP +\fB\-\-output\-strands\fR +output coverage and stats separately for each strand +.TP +\fB\-\-format\fR=\fI\,CHOICE\/\fR +output format +.SH COPYRIGHT +Copyright \(co 2014\-2019 Giovanni Birolo and Andrea Telatin +https://github.com/telatin/covtobed \- License MIT. +.br +This is free software: you are free to change and redistribute it. +There is NO WARRANTY, to the extent permitted by law. +.SH "SEE ALSO" +The full documentation for +.B covtobed +is maintained as a Texinfo manual. If the +.B info +and +.B covtobed +programs are properly installed at your site, the command +.IP +.B info covtobed +.PP +should give you access to the complete manual. View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/commit/43ec387a5019a2ba4d4d8353ad67d1ee1b101348 -- View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/commit/43ec387a5019a2ba4d4d8353ad67d1ee1b101348 You're receiving this email because of your account on salsa.debian.org.
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